2016-01-25 18:38:38 0.6 STATUS STARTED RnBeads Pipeline 2016-01-25 18:38:39 0.6 INFO Initialized report index and saved to index.html 2016-01-25 18:38:39 0.6 STATUS STARTED Loading Data 2016-01-25 18:38:39 0.6 INFO Number of cores: 1 2016-01-25 18:38:39 0.6 INFO Loading data of type "bs.bed.dir" 2016-01-25 18:38:39 0.6 STATUS STARTED Performing loading test 2016-01-25 18:38:39 0.6 INFO The first 10000 rows will be read from each data file 2016-01-25 18:38:39 0.6 INFO No column with file names specified: will try to find one 2016-01-25 18:38:39 0.6 STATUS STARTED Loading Data From BED Files 2016-01-25 18:38:40 0.7 STATUS STARTED Automatically parsing the provided sample annotation file 2016-01-25 18:38:40 0.7 STATUS Potential file names found in column 3 of the supplied annotation table 2016-01-25 18:38:40 0.7 STATUS COMPLETED Automatically parsing the provided sample annotation file 2016-01-25 18:38:42 0.7 STATUS Read 14 BED files 2016-01-25 18:38:43 0.7 STATUS Combined a data matrix with 15345 sites and 14 samples 2016-01-25 18:38:43 0.7 STATUS Processed all BED files 2016-01-25 18:38:43 0.7 STATUS STARTED Creating RnBiseqSet object 2016-01-25 18:38:55 2.0 STATUS Matched 15345 of 15345 methylation sites to the annotation 2016-01-25 18:38:55 2.0 STATUS Checking site coverage 2016-01-25 18:38:55 2.0 STATUS Creating methylation matrix 2016-01-25 18:38:55 2.0 STATUS Creating coverage matrix 2016-01-25 18:38:55 2.0 STATUS Creating object 2016-01-25 18:38:55 2.0 STATUS Summarizing strand methylation 2016-01-25 18:39:24 2.5 STATUS Summarizing tiling methylation 2016-01-25 18:39:24 2.5 STATUS Summarizing genes methylation 2016-01-25 18:39:24 2.5 STATUS Summarizing promoters methylation 2016-01-25 18:39:24 2.5 STATUS Summarizing cpgislands methylation 2016-01-25 18:39:24 2.5 STATUS COMPLETED Creating RnBiseqSet object 2016-01-25 18:39:24 2.5 STATUS COMPLETED Loading Data From BED Files 2016-01-25 18:39:24 2.5 STATUS STARTED Checking the loaded object 2016-01-25 18:39:24 2.5 INFO Checking the supplied RnBiseqSet object 2016-01-25 18:39:24 2.5 INFO The object contains information for 13807 methylation sites 2016-01-25 18:39:24 2.5 INFO The object contains information for 14 samples 2016-01-25 18:39:24 2.5 INFO The object contains 53298 missing methylation values 2016-01-25 18:39:24 2.5 INFO Methylation values are within the expected range 2016-01-25 18:39:24 2.5 INFO The object contains coverage information 2016-01-25 18:39:25 2.5 INFO Coverage values are within the expected range 2016-01-25 18:39:25 2.5 INFO The object loaded during the loading test is valid 2016-01-25 18:39:25 2.5 STATUS COMPLETED Checking the loaded object 2016-01-25 18:39:25 2.5 STATUS COMPLETED Performing loading test 2016-01-25 18:39:25 2.5 INFO No column with file names specified: will try to find one 2016-01-25 18:39:25 2.5 STATUS STARTED Loading Data From BED Files 2016-01-25 18:39:25 2.5 STATUS STARTED Automatically parsing the provided sample annotation file 2016-01-25 18:39:25 2.5 STATUS Potential file names found in column 3 of the supplied annotation table 2016-01-25 18:39:25 2.5 STATUS COMPLETED Automatically parsing the provided sample annotation file 2016-01-25 18:41:22 3.0 STATUS Read 14 BED files 2016-01-25 18:41:40 3.8 STATUS Combined a data matrix with 2198525 sites and 14 samples 2016-01-25 18:41:40 3.8 STATUS Processed all BED files 2016-01-25 18:41:40 3.8 STATUS STARTED Creating RnBiseqSet object 2016-01-25 18:42:11 3.6 STATUS Matched 2198525 of 2198525 methylation sites to the annotation 2016-01-25 18:42:11 3.6 STATUS Checking site coverage 2016-01-25 18:42:14 3.7 STATUS Creating methylation matrix 2016-01-25 18:42:19 3.8 STATUS Creating coverage matrix 2016-01-25 18:42:25 3.8 STATUS Creating object 2016-01-25 18:42:25 3.8 STATUS Summarizing strand methylation 2016-01-25 18:45:07 3.8 STATUS Summarizing tiling methylation 2016-01-25 18:45:58 3.8 STATUS Summarizing genes methylation 2016-01-25 18:46:08 3.8 STATUS Summarizing promoters methylation 2016-01-25 18:46:16 4.2 STATUS Summarizing cpgislands methylation 2016-01-25 18:46:23 3.8 STATUS COMPLETED Creating RnBiseqSet object 2016-01-25 18:46:23 3.8 STATUS COMPLETED Loading Data From BED Files 2016-01-25 18:46:23 3.8 STATUS Loaded data from /DEEP_fhgfs/projects/RnBeads/tutorial/Epigenomics2016/epigenomics2016/data/Bock2012_MolCell_RRBS/dataset/bed 2016-01-25 18:46:24 3.8 STATUS Added data loading section to the report 2016-01-25 18:46:24 3.8 STATUS Loaded 14 samples and 1975284 sites 2016-01-25 18:46:24 3.8 INFO Output object is of type RnBiseqSet 2016-01-25 18:46:24 3.8 STATUS COMPLETED Loading Data 2016-01-25 18:46:48 3.8 INFO Initialized report index and saved to index.html 2016-01-25 18:46:48 3.8 STATUS STARTED Quality Control 2016-01-25 18:46:48 3.8 INFO Number of cores: 1 2016-01-25 18:46:48 3.8 STATUS STARTED Preparing Quality Control Information 2016-01-25 18:46:48 3.8 STATUS COMPLETED Preparing Quality Control Information 2016-01-25 18:46:48 3.8 STATUS STARTED Quality Control Section 2016-01-25 18:52:46 3.7 STATUS Added sequencing coverage histograms 2016-01-25 18:53:21 4.5 STATUS Added sample coverage section 2016-01-25 18:54:13 7.6 STATUS Added sequencing coverage violin plots 2016-01-25 18:54:17 7.6 STATUS COMPLETED Quality Control Section 2016-01-25 18:54:17 7.6 STATUS COMPLETED Quality Control 2016-01-25 18:54:17 7.6 INFO Initialized report index and saved to index.html 2016-01-25 18:54:17 7.6 STATUS STARTED Preprocessing 2016-01-25 18:54:17 7.6 INFO Number of cores: 1 2016-01-25 18:54:17 7.6 STATUS STARTED Filtering Procedures 2016-01-25 18:54:36 5.9 STATUS STARTED Removal of SNP-enriched Sites 2016-01-25 18:54:36 5.9 STATUS Added a corresponding section to the report 2016-01-25 18:54:36 5.9 STATUS COMPLETED Removal of SNP-enriched Sites 2016-01-25 18:54:36 5.9 STATUS STARTED Removal of High Coverage (Outlier) Sites 2016-01-25 18:54:42 6.5 STATUS Removed 434 high coverage outlier sites 2016-01-25 18:54:42 6.5 STATUS Saved removed sites to /DEEP_fhgfs/projects/RnBeads/tutorial/Epigenomics2016/epigenomics2016/results/report_Bock2012_vanilla/preprocessing_data/removed_sites_high_coverage.csv 2016-01-25 18:54:42 6.5 STATUS Added a corresponding section to the report 2016-01-25 18:54:42 6.5 STATUS COMPLETED Removal of High Coverage (Outlier) Sites 2016-01-25 18:54:42 6.5 STATUS STARTED Replacing Low Coverage Sites by NA 2016-01-25 18:54:45 7.8 STATUS Masked 3143364 site(s) based on coverage threshold 5 2016-01-25 18:54:45 7.8 STATUS Saved numbers of masked sites per sample to /DEEP_fhgfs/projects/RnBeads/tutorial/Epigenomics2016/epigenomics2016/results/report_Bock2012_vanilla/preprocessing_data/masked_sites_coverage.csv 2016-01-25 18:54:45 7.8 STATUS Added a corresponding section to the report 2016-01-25 18:54:45 7.8 STATUS COMPLETED Replacing Low Coverage Sites by NA 2016-01-25 18:54:46 7.0 STATUS STARTED Missing Value Removal 2016-01-25 18:54:46 7.0 STATUS Using a sample quantile threshold of 0.5 2016-01-25 18:54:47 7.0 STATUS Removed 579135 site(s) with too many missing values 2016-01-25 18:54:48 7.0 STATUS Saved removed sites to /DEEP_fhgfs/projects/RnBeads/tutorial/Epigenomics2016/epigenomics2016/results/report_Bock2012_vanilla/preprocessing_data/removed_sites_na.csv 2016-01-25 18:54:53 7.3 STATUS Added a corresponding section to the report 2016-01-25 18:54:53 7.3 STATUS COMPLETED Missing Value Removal 2016-01-25 18:54:53 7.3 STATUS Retained 14 samples and 1395715 sites 2016-01-25 18:54:53 7.3 STATUS COMPLETED Filtering Procedures 2016-01-25 18:54:53 7.3 STATUS STARTED Summary of Filtering Procedures 2016-01-25 18:54:53 7.3 STATUS Creating summary table of removed sites, samples and unreliable measurements... 2016-01-25 18:54:54 7.3 STATUS Saving table and figures... 2016-01-25 18:54:55 7.3 STATUS Added summary table of removed and retained items 2016-01-25 18:54:57 7.7 STATUS Constructed sequences of removed and retained methylation values 2016-01-25 18:55:05 7.7 STATUS Added comparison between removed and retained beta values 2016-01-25 18:55:05 7.7 STATUS COMPLETED Summary of Filtering Procedures 2016-01-25 18:55:05 7.7 STATUS STARTED Manipulating the object 2016-01-25 18:56:14 6.9 STATUS Removed 579569 sites (probes) 2016-01-25 18:56:14 6.9 STATUS COMPLETED Manipulating the object 2016-01-25 18:56:14 6.9 STATUS COMPLETED Preprocessing 2016-01-25 18:56:34 6.9 INFO Initialized report index and saved to index.html 2016-01-25 18:56:34 6.9 STATUS STARTED Tracks and Tables 2016-01-25 18:56:34 6.9 INFO Number of cores: 1 2016-01-25 18:56:34 6.9 STATUS STARTED Generating Tracks and Tables 2016-01-25 18:56:34 6.9 STATUS STARTED Exporting sites 2016-01-25 18:56:34 6.9 STATUS STARTED Creating Track Hub -- bigBed 2016-01-25 18:56:34 6.9 STATUS STARTED Conversion to BED 2016-01-25 18:56:34 6.9 STATUS Converting to GRangesList 2016-01-25 18:56:58 7.6 STATUS Exporting sample HSC_1 2016-01-25 18:57:09 7.6 STATUS Exporting sample HSC_2 2016-01-25 18:57:19 7.6 STATUS Exporting sample CLP_1 2016-01-25 18:57:29 7.6 STATUS Exporting sample CLP_2 2016-01-25 18:57:40 7.6 STATUS Exporting sample CMP_1 2016-01-25 18:57:50 7.6 STATUS Exporting sample CMP_2 2016-01-25 18:58:00 7.6 STATUS Exporting sample CD4_1 2016-01-25 18:58:10 7.6 STATUS Exporting sample CD4_2 2016-01-25 18:58:21 7.7 STATUS Exporting sample B_cell_1 2016-01-25 18:58:31 7.7 STATUS Exporting sample B_cell_2 2016-01-25 18:58:41 7.7 STATUS Exporting sample Eryth_1 2016-01-25 18:58:50 7.7 STATUS Exporting sample Eryth_2 2016-01-25 18:58:56 7.7 STATUS Exporting sample Mono_1 2016-01-25 18:59:05 7.7 STATUS Exporting sample Mono_2 2016-01-25 18:59:12 7.7 STATUS COMPLETED Conversion to BED 2016-01-25 18:59:12 7.7 STATUS STARTED Creating Track Hub 2016-01-25 19:00:43 7.2 STATUS COMPLETED Creating Track Hub 2016-01-25 19:00:43 7.2 STATUS COMPLETED Creating Track Hub -- bigBed 2016-01-25 19:00:43 7.2 STATUS STARTED Creating UCSC Track Hub -- bigWig 2016-01-25 19:00:43 7.2 STATUS STARTED Conversion to bedGraph 2016-01-25 19:01:55 6.1 STATUS COMPLETED Conversion to bedGraph 2016-01-25 19:01:55 6.1 STATUS STARTED Creating Track Hub 2016-01-25 19:02:36 6.1 STATUS COMPLETED Creating Track Hub 2016-01-25 19:02:36 6.1 STATUS COMPLETED Creating UCSC Track Hub -- bigWig 2016-01-25 19:02:36 6.1 STATUS COMPLETED Exporting sites 2016-01-25 19:02:36 6.1 STATUS COMPLETED Generating Tracks and Tables 2016-01-25 19:02:36 6.1 STATUS STARTED Writing export report 2016-01-25 19:03:05 6.1 STATUS COMPLETED Writing export report 2016-01-25 19:03:05 6.1 STATUS COMPLETED Tracks and Tables 2016-01-25 19:03:05 6.1 INFO Initialized report index and saved to index.html 2016-01-25 19:03:05 6.1 STATUS STARTED Exploratory Analysis 2016-01-25 19:03:05 6.1 INFO Number of cores: 1 2016-01-25 19:03:06 6.1 STATUS Designed color mappings for probe type and CGI status 2016-01-25 19:04:48 6.0 STATUS STARTED Dimension Reduction Techniques 2016-01-25 19:04:49 6.7 STATUS STARTED MDS 2016-01-25 19:04:51 6.7 STATUS Calculated MDS coordinates using manhattan distance 2016-01-25 19:04:52 6.7 STATUS Calculated MDS coordinates using euclidean distance 2016-01-25 19:04:52 6.7 STATUS COMPLETED MDS 2016-01-25 19:04:52 6.7 STATUS STARTED PCA 2016-01-25 19:04:53 6.3 INFO Removed 644109 loci ( sites ) because they contain missing values 2016-01-25 19:04:55 6.3 STATUS COMPLETED PCA 2016-01-25 19:04:55 6.3 STATUS STARTED MDS 2016-01-25 19:04:55 6.3 STATUS Calculated MDS coordinates using manhattan distance 2016-01-25 19:04:55 6.3 STATUS Calculated MDS coordinates using euclidean distance 2016-01-25 19:04:55 6.3 STATUS COMPLETED MDS 2016-01-25 19:04:55 6.3 STATUS STARTED PCA 2016-01-25 19:04:55 6.3 INFO Removed 35347 loci ( tiling ) because they contain missing values 2016-01-25 19:04:56 6.3 STATUS COMPLETED PCA 2016-01-25 19:04:56 6.3 STATUS STARTED MDS 2016-01-25 19:04:56 6.3 STATUS Calculated MDS coordinates using manhattan distance 2016-01-25 19:04:56 6.3 STATUS Calculated MDS coordinates using euclidean distance 2016-01-25 19:04:56 6.3 STATUS COMPLETED MDS 2016-01-25 19:04:56 6.3 STATUS STARTED PCA 2016-01-25 19:04:56 6.3 INFO Removed 1397 loci ( genes ) because they contain missing values 2016-01-25 19:04:56 6.3 STATUS COMPLETED PCA 2016-01-25 19:04:56 6.3 STATUS STARTED MDS 2016-01-25 19:04:56 6.3 STATUS Calculated MDS coordinates using manhattan distance 2016-01-25 19:04:56 6.3 STATUS Calculated MDS coordinates using euclidean distance 2016-01-25 19:04:56 6.3 STATUS COMPLETED MDS 2016-01-25 19:04:56 6.3 STATUS STARTED PCA 2016-01-25 19:04:56 6.3 INFO Removed 1824 loci ( promoters ) because they contain missing values 2016-01-25 19:04:56 6.3 STATUS COMPLETED PCA 2016-01-25 19:04:56 6.3 STATUS STARTED MDS 2016-01-25 19:04:56 6.3 STATUS Calculated MDS coordinates using manhattan distance 2016-01-25 19:04:56 6.3 STATUS Calculated MDS coordinates using euclidean distance 2016-01-25 19:04:56 6.3 STATUS COMPLETED MDS 2016-01-25 19:04:56 6.3 STATUS STARTED PCA 2016-01-25 19:04:56 6.3 INFO Removed 648 loci ( cpgislands ) because they contain missing values 2016-01-25 19:04:56 6.3 STATUS COMPLETED PCA 2016-01-25 19:04:56 6.3 INFO Mapping 4 traits to point colors and types 2016-01-25 19:16:59 6.0 INFO Principal components that explain at least 95 % of the total variance: 11 2016-01-25 19:16:59 6.0 INFO Saved percentage of total variance to pca_variance_explained_1.csv 2016-01-25 19:17:00 6.0 INFO Principal components that explain at least 95 % of the total variance: 10 2016-01-25 19:17:00 6.0 INFO Saved percentage of total variance to pca_variance_explained_2.csv 2016-01-25 19:17:01 6.0 INFO Principal components that explain at least 95 % of the total variance: 9 2016-01-25 19:17:01 6.0 INFO Saved percentage of total variance to pca_variance_explained_3.csv 2016-01-25 19:17:02 6.0 INFO Principal components that explain at least 95 % of the total variance: 10 2016-01-25 19:17:02 6.0 INFO Saved percentage of total variance to pca_variance_explained_4.csv 2016-01-25 19:17:03 6.0 INFO Principal components that explain at least 95 % of the total variance: 9 2016-01-25 19:17:03 6.0 INFO Saved percentage of total variance to pca_variance_explained_5.csv 2016-01-25 19:17:05 6.0 STATUS Created scatter plots and CDFs summarizing the reduced dimensional representations 2016-01-25 19:17:05 6.0 STATUS COMPLETED Dimension Reduction Techniques 2016-01-25 19:17:05 6.0 STATUS STARTED Tests for Associations 2016-01-25 19:17:05 6.0 INFO Testing the following traits for associations: description; differentiation_level; blood_lineage; cmp_blood_CLP_CMP 2016-01-25 19:17:05 6.0 STATUS Computed correlations between principal components and traits. 2016-01-25 19:17:09 6.0 STATUS Computed pairwise correlations between traits. 2016-01-25 19:17:09 6.0 STATUS COMPLETED Tests for Associations 2016-01-25 19:17:37 6.0 STATUS STARTED Methylation Value Distributions - Sample Groups 2016-01-25 19:17:37 6.0 INFO processing beta_density_samples_1_1 2016-01-25 19:17:37 6.1 INFO Density estimation ( all samples--sites ): Groupwise retained observations after missing value removal: all:17667922/19540010 2016-01-25 19:17:37 6.1 INFO Density estimation ( all samples--sites ): Groupwise retained observations after subsampling: all:1000000/17667922 2016-01-25 19:17:40 6.1 INFO processing beta_density_samples_1_2 2016-01-25 19:17:40 6.1 INFO Density estimation ( all samples--tiling ): Groupwise retained observations after missing value removal: all:2326627/2417380 2016-01-25 19:17:40 6.1 INFO Density estimation ( all samples--tiling ): Groupwise retained observations after subsampling: all:1000000/2326627 2016-01-25 19:17:43 6.0 INFO processing beta_density_samples_1_3 2016-01-25 19:17:43 6.0 INFO Density estimation ( all samples--genes ): Groupwise retained observations after missing value removal: all:307509/311052 2016-01-25 19:17:44 6.0 INFO processing beta_density_samples_1_4 2016-01-25 19:17:44 6.0 INFO Density estimation ( all samples--promoters ): Groupwise retained observations after missing value removal: all:272299/277158 2016-01-25 19:17:45 6.0 INFO processing beta_density_samples_1_5 2016-01-25 19:17:45 6.0 INFO Density estimation ( all samples--cpgislands ): Groupwise retained observations after missing value removal: all:203873/205492 2016-01-25 19:17:46 6.0 INFO processing beta_density_samples_2_1 2016-01-25 19:17:46 6.0 INFO Density estimation ( description--sites ): Groupwise retained observations after missing value removal: B-cell:2738237/2791430; Common lymphoid progenitor:2695839/2791430; Common myeloid progenitor:2741148/2791430; Erythrocyte:2043134/2791430; Hematopoietic stem cell:2512281/2791430; Monocyte:2197140/2791430; T helper cell (CD4+):2740143/2791430 2016-01-25 19:17:47 6.0 INFO Density estimation ( description--sites ): Groupwise retained observations after subsampling: B-cell:1084885/2738237; Common lymphoid progenitor:1068087/2695839; Common myeloid progenitor:1086038/2741148; Erythrocyte:809486/2043134; Hematopoietic stem cell:995361/2512281; Monocyte:870503/2197140; T helper cell (CD4+):1085640/2740143 2016-01-25 19:18:04 6.0 INFO processing beta_density_samples_2_2 2016-01-25 19:18:04 6.0 INFO Density estimation ( description--tiling ): Groupwise retained observations after missing value removal: B-cell:341914/345340; Common lymphoid progenitor:338457/345340; Common myeloid progenitor:342383/345340; Erythrocyte:315806/345340; Hematopoietic stem cell:317245/345340; Monocyte:329259/345340; T helper cell (CD4+):341563/345340 2016-01-25 19:18:11 6.0 INFO processing beta_density_samples_2_3 2016-01-25 19:18:11 6.0 INFO Density estimation ( description--genes ): Groupwise retained observations after missing value removal: B-cell:44295/44436; Common lymphoid progenitor:44213/44436; Common myeloid progenitor:44324/44436; Erythrocyte:43343/44436; Hematopoietic stem cell:43263/44436; Monocyte:43768/44436; T helper cell (CD4+):44303/44436 2016-01-25 19:18:13 6.0 INFO processing beta_density_samples_2_4 2016-01-25 19:18:13 6.0 INFO Density estimation ( description--promoters ): Groupwise retained observations after missing value removal: B-cell:39420/39594; Common lymphoid progenitor:39260/39594; Common myeloid progenitor:39406/39594; Erythrocyte:38125/39594; Hematopoietic stem cell:38023/39594; Monocyte:38667/39594; T helper cell (CD4+):39398/39594 2016-01-25 19:18:14 6.0 INFO processing beta_density_samples_2_5 2016-01-25 19:18:14 6.0 INFO Density estimation ( description--cpgislands ): Groupwise retained observations after missing value removal: B-cell:29306/29356; Common lymphoid progenitor:29265/29356; Common myeloid progenitor:29301/29356; Erythrocyte:28801/29356; Hematopoietic stem cell:28914/29356; Monocyte:28982/29356; T helper cell (CD4+):29304/29356 2016-01-25 19:18:16 6.0 INFO processing beta_density_samples_3_1 2016-01-25 19:18:16 6.0 INFO Density estimation ( differentiation_level--sites ): Groupwise retained observations after missing value removal: differentiated:9718654/11165720; progenitor:5436987/5582860; stemCell:2512281/2791430 2016-01-25 19:18:16 6.0 INFO Density estimation ( differentiation_level--sites ): Groupwise retained observations after subsampling: differentiated:1650220/9718654; progenitor:923196/5436987; stemCell:426583/2512281 2016-01-25 19:18:25 6.0 INFO processing beta_density_samples_3_2 2016-01-25 19:18:25 6.0 INFO Density estimation ( differentiation_level--tiling ): Groupwise retained observations after missing value removal: differentiated:1328542/1381360; progenitor:680840/690680; stemCell:317245/345340 2016-01-25 19:18:31 6.0 INFO processing beta_density_samples_3_3 2016-01-25 19:18:31 6.0 INFO Density estimation ( differentiation_level--genes ): Groupwise retained observations after missing value removal: differentiated:175709/177744; progenitor:88537/88872; stemCell:43263/44436 2016-01-25 19:18:32 6.0 INFO processing beta_density_samples_3_4 2016-01-25 19:18:32 6.0 INFO Density estimation ( differentiation_level--promoters ): Groupwise retained observations after missing value removal: differentiated:155610/158376; progenitor:78666/79188; stemCell:38023/39594 2016-01-25 19:18:34 6.0 INFO processing beta_density_samples_3_5 2016-01-25 19:18:34 6.0 INFO Density estimation ( differentiation_level--cpgislands ): Groupwise retained observations after missing value removal: differentiated:116393/117424; progenitor:58566/58712; stemCell:28914/29356 2016-01-25 19:18:35 6.0 INFO processing beta_density_samples_4_1 2016-01-25 19:18:36 6.0 INFO Density estimation ( blood_lineage--sites ): Groupwise retained observations after missing value removal: lymphoid:8174219/8374290; myeloid:6981422/8374290 2016-01-25 19:18:36 6.0 INFO Density estimation ( blood_lineage--sites ): Groupwise retained observations after subsampling: lymphoid:1078703/8174219; myeloid:921297/6981422 2016-01-25 19:18:41 6.0 INFO processing beta_density_samples_4_2 2016-01-25 19:18:41 6.0 INFO Density estimation ( blood_lineage--tiling ): Groupwise retained observations after missing value removal: lymphoid:1021934/1036020; myeloid:987448/1036020 2016-01-25 19:18:41 6.0 INFO Density estimation ( blood_lineage--tiling ): Groupwise retained observations after subsampling: lymphoid:1017162/1021934; myeloid:982838/987448 2016-01-25 19:18:46 6.0 INFO processing beta_density_samples_4_3 2016-01-25 19:18:46 6.0 INFO Density estimation ( blood_lineage--genes ): Groupwise retained observations after missing value removal: lymphoid:132811/133308; myeloid:131435/133308 2016-01-25 19:18:48 6.0 INFO processing beta_density_samples_4_4 2016-01-25 19:18:48 6.0 INFO Density estimation ( blood_lineage--promoters ): Groupwise retained observations after missing value removal: lymphoid:118078/118782; myeloid:116198/118782 2016-01-25 19:18:49 6.0 INFO processing beta_density_samples_4_5 2016-01-25 19:18:49 6.0 INFO Density estimation ( blood_lineage--cpgislands ): Groupwise retained observations after missing value removal: lymphoid:87875/88068; myeloid:87084/88068 2016-01-25 19:18:50 6.0 INFO processing beta_density_samples_5_1 2016-01-25 19:18:51 6.1 INFO Density estimation ( cmp_blood_CLP_CMP--sites ): Groupwise retained observations after missing value removal: CLP:2695839/2791430; CMP:2741148/2791430 2016-01-25 19:18:51 6.0 INFO Density estimation ( cmp_blood_CLP_CMP--sites ): Groupwise retained observations after subsampling: CLP:991667/2695839; CMP:1008333/2741148 2016-01-25 19:18:56 6.0 INFO processing beta_density_samples_5_2 2016-01-25 19:18:56 6.0 INFO Density estimation ( cmp_blood_CLP_CMP--tiling ): Groupwise retained observations after missing value removal: CLP:338457/345340; CMP:342383/345340 2016-01-25 19:18:59 6.0 INFO processing beta_density_samples_5_3 2016-01-25 19:18:59 6.0 INFO Density estimation ( cmp_blood_CLP_CMP--genes ): Groupwise retained observations after missing value removal: CLP:44213/44436; CMP:44324/44436 2016-01-25 19:19:00 6.0 INFO processing beta_density_samples_5_4 2016-01-25 19:19:00 6.0 INFO Density estimation ( cmp_blood_CLP_CMP--promoters ): Groupwise retained observations after missing value removal: CLP:39260/39594; CMP:39406/39594 2016-01-25 19:19:00 6.0 INFO processing beta_density_samples_5_5 2016-01-25 19:19:00 6.0 INFO Density estimation ( cmp_blood_CLP_CMP--cpgislands ): Groupwise retained observations after missing value removal: CLP:29265/29356; CMP:29301/29356 2016-01-25 19:19:01 6.0 STATUS COMPLETED Methylation Value Distributions - Sample Groups 2016-01-25 19:19:01 6.0 STATUS STARTED Methylation Value Distributions - Site Categories 2016-01-25 19:19:03 6.0 INFO Density estimation ( CGI Relation--all samples ): Groupwise retained observations after missing value removal: Open Sea:11113880/12362126; Shelf:80846/89600; Shore:105564/116592; Island:6367632/6971692 2016-01-25 19:19:03 6.0 INFO Density estimation ( CGI Relation--all samples ): Groupwise retained observations after subsampling: Open Sea:2516171/11113880; Shelf:18303/80846; Shore:23900/105564; Island:1441626/6367632 2016-01-25 19:19:14 6.0 INFO Density estimation ( CGI Relation--B-cell (based on description) ): Groupwise retained observations after missing value removal: Open Sea:1723533/1766018; Shelf:12451/12800; Shore:16208/16656; Island:986045/995956 2016-01-25 19:19:21 6.0 INFO Density estimation ( CGI Relation--Common lymphoid progenitor (based on description) ): Groupwise retained observations after missing value removal: Open Sea:1690086/1766018; Shelf:12227/12800; Shore:15813/16656; Island:977713/995956 2016-01-25 19:19:29 6.0 INFO Density estimation ( CGI Relation--Common myeloid progenitor (based on description) ): Groupwise retained observations after missing value removal: Open Sea:1729626/1766018; Shelf:12512/12800; Shore:16170/16656; Island:982840/995956 2016-01-25 19:19:36 6.0 INFO Density estimation ( CGI Relation--Erythrocyte (based on description) ): Groupwise retained observations after missing value removal: Open Sea:1305051/1766018; Shelf:9737/12800; Shore:12924/16656; Island:715422/995956 2016-01-25 19:19:42 6.0 INFO Density estimation ( CGI Relation--Hematopoietic stem cell (based on description) ): Groupwise retained observations after missing value removal: Open Sea:1521630/1766018; Shelf:11224/12800; Shore:14671/16656; Island:964756/995956 2016-01-25 19:19:49 6.0 INFO Density estimation ( CGI Relation--Monocyte (based on description) ): Groupwise retained observations after missing value removal: Open Sea:1419481/1766018; Shelf:10201/12800; Shore:13642/16656; Island:753816/995956 2016-01-25 19:19:56 6.0 INFO Density estimation ( CGI Relation--T helper cell (CD4+) (based on description) ): Groupwise retained observations after missing value removal: Open Sea:1724473/1766018; Shelf:12494/12800; Shore:16136/16656; Island:987040/995956 2016-01-25 19:20:04 6.0 INFO Density estimation ( CGI Relation--differentiated (based on differentiation_level) ): Groupwise retained observations after missing value removal: Open Sea:6172538/7064072; Shelf:44883/51200; Shore:58910/66624; Island:3442323/3983824 2016-01-25 19:20:04 6.0 INFO Density estimation ( CGI Relation--differentiated (based on differentiation_level) ): Groupwise retained observations after subsampling: Open Sea:2540491/6172538; Shelf:18473/44883; Shore:24246/58910; Island:1416790/3442323 2016-01-25 19:20:15 6.0 INFO Density estimation ( CGI Relation--progenitor (based on differentiation_level) ): Groupwise retained observations after missing value removal: Open Sea:3419712/3532036; Shelf:24739/25600; Shore:31983/33312; Island:1960553/1991912 2016-01-25 19:20:15 6.0 INFO Density estimation ( CGI Relation--progenitor (based on differentiation_level) ): Groupwise retained observations after subsampling: Open Sea:2515888/3419712; Shelf:18201/24739; Shore:23530/31983; Island:1442382/1960553 2016-01-25 19:20:26 6.0 INFO Density estimation ( CGI Relation--stemCell (based on differentiation_level) ): Groupwise retained observations after missing value removal: Open Sea:1521630/1766018; Shelf:11224/12800; Shore:14671/16656; Island:964756/995956 2016-01-25 19:20:33 6.0 INFO Density estimation ( CGI Relation--lymphoid (based on blood_lineage) ): Groupwise retained observations after missing value removal: Open Sea:5138092/5298054; Shelf:37172/38400; Shore:48157/49968; Island:2950798/2987868 2016-01-25 19:20:34 6.0 INFO Density estimation ( CGI Relation--lymphoid (based on blood_lineage) ): Groupwise retained observations after subsampling: Open Sea:2514291/5138092; Shelf:18190/37172; Shore:23565/48157; Island:1443953/2950798 2016-01-25 19:20:44 6.0 INFO Density estimation ( CGI Relation--myeloid (based on blood_lineage) ): Groupwise retained observations after missing value removal: Open Sea:4454158/5298054; Shelf:32450/38400; Shore:42736/49968; Island:2452078/2987868 2016-01-25 19:20:45 6.0 INFO Density estimation ( CGI Relation--myeloid (based on blood_lineage) ): Groupwise retained observations after subsampling: Open Sea:2552006/4454158; Shelf:18592/32450; Shore:24486/42736; Island:1404916/2452078 2016-01-25 19:20:55 6.0 INFO Density estimation ( CGI Relation--CLP (based on cmp_blood_CLP_CMP) ): Groupwise retained observations after missing value removal: Open Sea:1690086/1766018; Shelf:12227/12800; Shore:15813/16656; Island:977713/995956 2016-01-25 19:21:03 6.0 INFO Density estimation ( CGI Relation--CMP (based on cmp_blood_CLP_CMP) ): Groupwise retained observations after missing value removal: Open Sea:1729626/1766018; Shelf:12512/12800; Shore:16170/16656; Island:982840/995956 2016-01-25 19:21:10 6.0 STATUS COMPLETED Methylation Value Distributions - Site Categories 2016-01-25 19:21:11 6.3 STATUS STARTED Scatter Plots of Mean Beta vs Variance 2016-01-25 19:21:11 6.3 INFO Sample subgroups are defined by: description; differentiation_level; blood_lineage; cmp_blood_CLP_CMP 2016-01-25 19:35:48 6.1 WARNING Removed 51050 loci with missing values in group B-cell (based on description) 2016-01-25 19:49:47 6.1 WARNING Removed 91064 loci with missing values in group Common lymphoid progenitor (based on description) 2016-01-25 20:03:21 6.1 WARNING Removed 47479 loci with missing values in group Common myeloid progenitor (based on description) 2016-01-25 20:17:21 6.1 WARNING Removed 533084 loci with missing values in group Erythrocyte (based on description) 2016-01-25 20:26:21 6.1 WARNING Removed 176638 loci with missing values in group Hematopoietic stem cell (based on description) 2016-01-25 20:39:05 6.1 WARNING Removed 378988 loci with missing values in group Monocyte (based on description) 2016-01-25 20:49:41 6.1 WARNING Removed 49906 loci with missing values in group T helper cell (CD4+) (based on description) 2016-01-25 21:03:44 6.1 WARNING Removed 57 loci with missing values in group differentiated (based on differentiation_level) 2016-01-25 21:18:18 6.1 WARNING Removed 3853 loci with missing values in group progenitor (based on differentiation_level) 2016-01-25 21:32:47 6.1 WARNING Removed 176638 loci with missing values in group stemCell (based on differentiation_level) 2016-01-25 21:45:31 6.1 WARNING Removed 327 loci with missing values in group lymphoid (based on blood_lineage) 2016-01-25 22:00:04 6.1 WARNING Removed 6885 loci with missing values in group myeloid (based on blood_lineage) 2016-01-25 22:14:30 6.1 WARNING Removed 91064 loci with missing values in group CLP (based on cmp_blood_CLP_CMP) 2016-01-25 22:28:06 6.1 WARNING Removed 47479 loci with missing values in group CMP (based on cmp_blood_CLP_CMP) 2016-01-25 22:42:06 6.1 STATUS Created 45 scatter plots of methylation variance on the site level 2016-01-25 22:43:22 6.1 WARNING Removed 3314 loci with missing values in group B-cell (based on description) 2016-01-25 22:44:36 6.1 WARNING Removed 6666 loci with missing values in group Common lymphoid progenitor (based on description) 2016-01-25 22:45:49 6.1 WARNING Removed 2846 loci with missing values in group Common myeloid progenitor (based on description) 2016-01-25 22:47:03 6.1 WARNING Removed 25772 loci with missing values in group Erythrocyte (based on description) 2016-01-25 22:48:08 6.1 WARNING Removed 17481 loci with missing values in group Hematopoietic stem cell (based on description) 2016-01-25 22:49:17 6.1 WARNING Removed 12492 loci with missing values in group Monocyte (based on description) 2016-01-25 22:50:27 6.1 WARNING Removed 3701 loci with missing values in group T helper cell (CD4+) (based on description) 2016-01-25 22:51:41 6.1 WARNING Removed 1 loci with missing values in group differentiated (based on differentiation_level) 2016-01-25 22:52:57 6.1 WARNING Removed 159 loci with missing values in group progenitor (based on differentiation_level) 2016-01-25 22:54:12 6.1 WARNING Removed 17481 loci with missing values in group stemCell (based on differentiation_level) 2016-01-25 22:55:20 6.1 WARNING Removed 11 loci with missing values in group lymphoid (based on blood_lineage) 2016-01-25 22:56:36 6.1 WARNING Removed 125 loci with missing values in group myeloid (based on blood_lineage) 2016-01-25 22:57:52 6.1 WARNING Removed 6666 loci with missing values in group CLP (based on cmp_blood_CLP_CMP) 2016-01-25 22:59:04 6.1 WARNING Removed 2846 loci with missing values in group CMP (based on cmp_blood_CLP_CMP) 2016-01-25 23:00:31 6.1 WARNING Removed 132 loci with missing values in group B-cell (based on description) 2016-01-25 23:00:43 6.1 WARNING Removed 215 loci with missing values in group Common lymphoid progenitor (based on description) 2016-01-25 23:00:55 6.1 WARNING Removed 111 loci with missing values in group Common myeloid progenitor (based on description) 2016-01-25 23:01:07 6.1 WARNING Removed 956 loci with missing values in group Erythrocyte (based on description) 2016-01-25 23:01:19 6.1 WARNING Removed 744 loci with missing values in group Hematopoietic stem cell (based on description) 2016-01-25 23:01:31 6.1 WARNING Removed 516 loci with missing values in group Monocyte (based on description) 2016-01-25 23:01:43 6.1 WARNING Removed 132 loci with missing values in group T helper cell (CD4+) (based on description) 2016-01-25 23:02:07 6.1 WARNING Removed 4 loci with missing values in group progenitor (based on differentiation_level) 2016-01-25 23:02:20 6.1 WARNING Removed 744 loci with missing values in group stemCell (based on differentiation_level) 2016-01-25 23:02:44 6.1 WARNING Removed 3 loci with missing values in group myeloid (based on blood_lineage) 2016-01-25 23:02:56 6.1 WARNING Removed 215 loci with missing values in group CLP (based on cmp_blood_CLP_CMP) 2016-01-25 23:03:08 6.1 WARNING Removed 111 loci with missing values in group CMP (based on cmp_blood_CLP_CMP) 2016-01-25 23:03:31 6.1 WARNING Removed 171 loci with missing values in group B-cell (based on description) 2016-01-25 23:03:42 6.1 WARNING Removed 315 loci with missing values in group Common lymphoid progenitor (based on description) 2016-01-25 23:03:53 6.1 WARNING Removed 177 loci with missing values in group Common myeloid progenitor (based on description) 2016-01-25 23:04:04 6.1 WARNING Removed 1268 loci with missing values in group Erythrocyte (based on description) 2016-01-25 23:04:15 6.1 WARNING Removed 997 loci with missing values in group Hematopoietic stem cell (based on description) 2016-01-25 23:04:26 6.1 WARNING Removed 722 loci with missing values in group Monocyte (based on description) 2016-01-25 23:04:36 6.1 WARNING Removed 193 loci with missing values in group T helper cell (CD4+) (based on description) 2016-01-25 23:04:59 6.1 WARNING Removed 15 loci with missing values in group progenitor (based on differentiation_level) 2016-01-25 23:05:10 6.1 WARNING Removed 997 loci with missing values in group stemCell (based on differentiation_level) 2016-01-25 23:05:32 6.1 WARNING Removed 11 loci with missing values in group myeloid (based on blood_lineage) 2016-01-25 23:05:44 6.1 WARNING Removed 315 loci with missing values in group CLP (based on cmp_blood_CLP_CMP) 2016-01-25 23:05:54 6.1 WARNING Removed 177 loci with missing values in group CMP (based on cmp_blood_CLP_CMP) 2016-01-25 23:06:15 6.1 WARNING Removed 46 loci with missing values in group B-cell (based on description) 2016-01-25 23:06:24 6.1 WARNING Removed 86 loci with missing values in group Common lymphoid progenitor (based on description) 2016-01-25 23:06:33 6.1 WARNING Removed 47 loci with missing values in group Common myeloid progenitor (based on description) 2016-01-25 23:06:42 6.1 WARNING Removed 488 loci with missing values in group Erythrocyte (based on description) 2016-01-25 23:06:51 6.1 WARNING Removed 284 loci with missing values in group Hematopoietic stem cell (based on description) 2016-01-25 23:07:00 6.1 WARNING Removed 290 loci with missing values in group Monocyte (based on description) 2016-01-25 23:07:08 6.1 WARNING Removed 51 loci with missing values in group T helper cell (CD4+) (based on description) 2016-01-25 23:07:26 6.1 WARNING Removed 7 loci with missing values in group progenitor (based on differentiation_level) 2016-01-25 23:07:36 6.1 WARNING Removed 284 loci with missing values in group stemCell (based on differentiation_level) 2016-01-25 23:07:53 6.1 WARNING Removed 5 loci with missing values in group myeloid (based on blood_lineage) 2016-01-25 23:08:02 6.1 WARNING Removed 86 loci with missing values in group CLP (based on cmp_blood_CLP_CMP) 2016-01-25 23:08:11 6.1 WARNING Removed 47 loci with missing values in group CMP (based on cmp_blood_CLP_CMP) 2016-01-25 23:08:20 6.1 STATUS Created 120 scatter plots of methylation variance on the region level 2016-01-25 23:08:20 6.1 STATUS COMPLETED Scatter Plots of Mean Beta vs Variance 2016-01-25 23:08:20 6.1 STATUS STARTED Sample Clustering 2016-01-25 23:08:20 6.1 STATUS STARTED Agglomerative Hierarchical Clustering 2016-01-25 23:08:25 6.4 STATUS Performed clustering on sites using correlation as a distance metric 2016-01-25 23:08:27 6.4 STATUS Performed clustering on sites using manhattan as a distance metric 2016-01-25 23:08:29 6.4 STATUS Performed clustering on sites using euclidean as a distance metric 2016-01-25 23:08:29 6.4 STATUS Performed clustering on tiling using correlation as a distance metric 2016-01-25 23:08:29 6.4 STATUS Performed clustering on tiling using manhattan as a distance metric 2016-01-25 23:08:30 6.4 STATUS Performed clustering on tiling using euclidean as a distance metric 2016-01-25 23:08:30 6.4 STATUS Performed clustering on genes using correlation as a distance metric 2016-01-25 23:08:30 6.4 STATUS Performed clustering on genes using manhattan as a distance metric 2016-01-25 23:08:30 6.4 STATUS Performed clustering on genes using euclidean as a distance metric 2016-01-25 23:08:30 6.4 STATUS Performed clustering on promoters using correlation as a distance metric 2016-01-25 23:08:30 6.4 STATUS Performed clustering on promoters using manhattan as a distance metric 2016-01-25 23:08:30 6.4 STATUS Performed clustering on promoters using euclidean as a distance metric 2016-01-25 23:08:30 6.4 STATUS Performed clustering on cpgislands using correlation as a distance metric 2016-01-25 23:08:30 6.4 STATUS Performed clustering on cpgislands using manhattan as a distance metric 2016-01-25 23:08:30 6.4 STATUS Performed clustering on cpgislands using euclidean as a distance metric 2016-01-25 23:08:30 6.4 STATUS COMPLETED Agglomerative Hierarchical Clustering 2016-01-25 23:08:31 6.3 STATUS STARTED Clustering Section 2016-01-25 23:08:32 6.3 STATUS STARTED Generating Heatmaps 2016-01-25 23:08:32 6.3 STATUS STARTED Region type: sites 2016-01-25 23:10:19 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage average . Discarding row dendrogram 2016-01-25 23:10:21 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage average . Discarding row dendrogram 2016-01-25 23:10:22 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage average . Discarding row dendrogram 2016-01-25 23:10:24 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage average . Discarding row dendrogram 2016-01-25 23:10:25 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage average . Discarding row dendrogram 2016-01-25 23:10:27 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage average . Discarding row dendrogram 2016-01-25 23:10:28 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage average . Discarding row dendrogram 2016-01-25 23:10:30 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage average . Discarding row dendrogram 2016-01-25 23:10:31 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage complete . Discarding row dendrogram 2016-01-25 23:10:33 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage complete . Discarding row dendrogram 2016-01-25 23:10:35 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage complete . Discarding row dendrogram 2016-01-25 23:10:36 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage complete . Discarding row dendrogram 2016-01-25 23:10:38 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage complete . Discarding row dendrogram 2016-01-25 23:10:39 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage complete . Discarding row dendrogram 2016-01-25 23:10:41 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage complete . Discarding row dendrogram 2016-01-25 23:10:42 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage complete . Discarding row dendrogram 2016-01-25 23:10:44 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage median . Discarding row dendrogram 2016-01-25 23:10:45 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage median . Discarding row dendrogram 2016-01-25 23:10:47 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage median . Discarding row dendrogram 2016-01-25 23:10:49 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage median . Discarding row dendrogram 2016-01-25 23:10:50 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage median . Discarding row dendrogram 2016-01-25 23:10:52 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage median . Discarding row dendrogram 2016-01-25 23:10:54 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage median . Discarding row dendrogram 2016-01-25 23:10:55 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage median . Discarding row dendrogram 2016-01-25 23:10:57 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage average . Discarding row dendrogram 2016-01-25 23:10:58 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage average . Discarding row dendrogram 2016-01-25 23:11:00 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage average . Discarding row dendrogram 2016-01-25 23:11:01 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage average . Discarding row dendrogram 2016-01-25 23:11:03 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage average . Discarding row dendrogram 2016-01-25 23:11:04 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage average . Discarding row dendrogram 2016-01-25 23:11:06 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage average . Discarding row dendrogram 2016-01-25 23:11:07 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage average . Discarding row dendrogram 2016-01-25 23:11:09 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage complete . Discarding row dendrogram 2016-01-25 23:11:11 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage complete . Discarding row dendrogram 2016-01-25 23:11:12 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage complete . Discarding row dendrogram 2016-01-25 23:11:14 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage complete . Discarding row dendrogram 2016-01-25 23:11:15 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage complete . Discarding row dendrogram 2016-01-25 23:11:17 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage complete . Discarding row dendrogram 2016-01-25 23:11:18 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage complete . Discarding row dendrogram 2016-01-25 23:11:20 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage complete . Discarding row dendrogram 2016-01-25 23:11:22 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage median . Discarding row dendrogram 2016-01-25 23:11:23 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage median . Discarding row dendrogram 2016-01-25 23:11:25 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage median . Discarding row dendrogram 2016-01-25 23:11:26 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage median . Discarding row dendrogram 2016-01-25 23:11:28 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage median . Discarding row dendrogram 2016-01-25 23:11:29 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage median . Discarding row dendrogram 2016-01-25 23:11:31 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage median . Discarding row dendrogram 2016-01-25 23:11:33 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage median . Discarding row dendrogram 2016-01-25 23:11:34 6.3 STATUS COMPLETED Region type: sites 2016-01-25 23:11:34 6.3 STATUS STARTED Region type: tiling 2016-01-25 23:13:16 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage average . Discarding row dendrogram 2016-01-25 23:13:18 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage average . Discarding row dendrogram 2016-01-25 23:13:19 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage average . Discarding row dendrogram 2016-01-25 23:13:21 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage average . Discarding row dendrogram 2016-01-25 23:13:22 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage average . Discarding row dendrogram 2016-01-25 23:13:24 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage average . Discarding row dendrogram 2016-01-25 23:13:26 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage average . Discarding row dendrogram 2016-01-25 23:13:27 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage average . Discarding row dendrogram 2016-01-25 23:13:29 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage complete . Discarding row dendrogram 2016-01-25 23:13:30 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage complete . Discarding row dendrogram 2016-01-25 23:13:32 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage complete . Discarding row dendrogram 2016-01-25 23:13:34 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage complete . Discarding row dendrogram 2016-01-25 23:13:35 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage complete . Discarding row dendrogram 2016-01-25 23:13:37 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage complete . Discarding row dendrogram 2016-01-25 23:13:38 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage complete . Discarding row dendrogram 2016-01-25 23:13:40 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage complete . Discarding row dendrogram 2016-01-25 23:13:41 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage median . Discarding row dendrogram 2016-01-25 23:13:43 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage median . Discarding row dendrogram 2016-01-25 23:13:44 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage median . Discarding row dendrogram 2016-01-25 23:13:46 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage median . Discarding row dendrogram 2016-01-25 23:13:48 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage median . Discarding row dendrogram 2016-01-25 23:13:49 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage median . Discarding row dendrogram 2016-01-25 23:13:51 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage median . Discarding row dendrogram 2016-01-25 23:13:52 6.3 WARNING Could not cluster rows of the heatmap with method manhattan and linkage median . Discarding row dendrogram 2016-01-25 23:13:54 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage average . Discarding row dendrogram 2016-01-25 23:13:55 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage average . Discarding row dendrogram 2016-01-25 23:13:57 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage average . Discarding row dendrogram 2016-01-25 23:13:58 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage average . Discarding row dendrogram 2016-01-25 23:14:00 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage average . Discarding row dendrogram 2016-01-25 23:14:01 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage average . Discarding row dendrogram 2016-01-25 23:14:03 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage average . Discarding row dendrogram 2016-01-25 23:14:05 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage average . Discarding row dendrogram 2016-01-25 23:14:06 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage complete . Discarding row dendrogram 2016-01-25 23:14:08 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage complete . Discarding row dendrogram 2016-01-25 23:14:09 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage complete . Discarding row dendrogram 2016-01-25 23:14:11 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage complete . Discarding row dendrogram 2016-01-25 23:14:12 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage complete . Discarding row dendrogram 2016-01-25 23:14:14 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage complete . Discarding row dendrogram 2016-01-25 23:14:16 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage complete . Discarding row dendrogram 2016-01-25 23:14:17 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage complete . Discarding row dendrogram 2016-01-25 23:14:19 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage median . Discarding row dendrogram 2016-01-25 23:14:20 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage median . Discarding row dendrogram 2016-01-25 23:14:22 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage median . Discarding row dendrogram 2016-01-25 23:14:23 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage median . Discarding row dendrogram 2016-01-25 23:14:25 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage median . Discarding row dendrogram 2016-01-25 23:14:26 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage median . Discarding row dendrogram 2016-01-25 23:14:28 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage median . Discarding row dendrogram 2016-01-25 23:14:29 6.3 WARNING Could not cluster rows of the heatmap with method euclidean and linkage median . Discarding row dendrogram 2016-01-25 23:14:31 6.3 STATUS COMPLETED Region type: tiling 2016-01-25 23:14:31 6.3 STATUS STARTED Region type: genes 2016-01-25 23:18:16 6.3 STATUS COMPLETED Region type: genes 2016-01-25 23:18:16 6.3 STATUS STARTED Region type: promoters 2016-01-25 23:21:59 6.3 STATUS COMPLETED Region type: promoters 2016-01-25 23:21:59 6.3 STATUS STARTED Region type: cpgislands 2016-01-25 23:25:44 6.3 STATUS COMPLETED Region type: cpgislands 2016-01-25 23:25:44 6.3 STATUS Created 540 heatmaps based on the clustering results 2016-01-25 23:25:44 6.3 STATUS COMPLETED Generating Heatmaps 2016-01-25 23:25:44 6.3 STATUS STARTED Adding Color Legends 2016-01-25 23:26:48 6.3 STATUS COMPLETED Adding Color Legends 2016-01-25 23:26:48 6.3 STATUS STARTED Estimating Optimal Numbers of Clusters 2016-01-25 23:27:07 6.3 STATUS Estimated number of clusters based on mean silhouette value 2016-01-25 23:27:07 6.3 STATUS COMPLETED Estimating Optimal Numbers of Clusters 2016-01-25 23:27:07 6.3 STATUS STARTED Overlapping Clusters with Sample Traits 2016-01-25 23:27:07 6.3 STATUS Computed adjusted rand indices and saved to exploratory_analysis_data/adjusted_rand_indices_1.csv 2016-01-25 23:27:08 6.3 STATUS Computed adjusted rand indices and saved to exploratory_analysis_data/adjusted_rand_indices_2.csv 2016-01-25 23:27:08 6.3 STATUS Computed adjusted rand indices and saved to exploratory_analysis_data/adjusted_rand_indices_3.csv 2016-01-25 23:27:08 6.3 STATUS Computed adjusted rand indices and saved to exploratory_analysis_data/adjusted_rand_indices_4.csv 2016-01-25 23:27:08 6.3 STATUS Computed adjusted rand indices and saved to exploratory_analysis_data/adjusted_rand_indices_5.csv 2016-01-25 23:27:25 6.3 STATUS COMPLETED Overlapping Clusters with Sample Traits 2016-01-25 23:27:25 6.3 STATUS COMPLETED Clustering Section 2016-01-25 23:27:25 6.3 STATUS COMPLETED Sample Clustering 2016-01-25 23:27:25 6.3 STATUS STARTED Drawing regional methylation profiles 2016-01-25 23:27:25 6.3 STATUS STARTED Creating a Corresponding Section in the Report 2016-01-25 23:27:45 6.6 INFO Subsampling 1000000 of 1543387 site occurences (region type: genes ) 2016-01-25 23:27:46 6.6 STATUS Plotting region profiles for region genes and column all samples ... 2016-01-25 23:32:18 14.4 STATUS Plotting region profiles for region genes and column description ... 2016-01-25 23:36:27 9.6 STATUS Plotting region profiles for region genes and column differentiation_level ... 2016-01-25 23:40:41 11.2 STATUS Plotting region profiles for region genes and column blood_lineage ... 2016-01-25 23:44:14 11.6 STATUS Plotting region profiles for region genes and column cmp_blood_CLP_CMP ... 2016-01-25 23:45:44 12.5 STATUS Plotting region profiles for region promoters and column all samples ... 2016-01-25 23:48:10 13.0 STATUS Plotting region profiles for region promoters and column description ... 2016-01-25 23:50:34 9.6 STATUS Plotting region profiles for region promoters and column differentiation_level ... 2016-01-25 23:53:00 9.9 STATUS Plotting region profiles for region promoters and column blood_lineage ... 2016-01-25 23:55:02 9.3 STATUS Plotting region profiles for region promoters and column cmp_blood_CLP_CMP ... 2016-01-25 23:56:04 8.5 STATUS Plotting region profiles for region cpgislands and column all samples ... 2016-01-25 23:58:15 12.0 STATUS Plotting region profiles for region cpgislands and column description ... 2016-01-26 00:00:21 9.2 STATUS Plotting region profiles for region cpgislands and column differentiation_level ... 2016-01-26 00:02:30 9.1 STATUS Plotting region profiles for region cpgislands and column blood_lineage ... 2016-01-26 00:04:18 10.3 STATUS Plotting region profiles for region cpgislands and column cmp_blood_CLP_CMP ... 2016-01-26 00:04:55 8.8 STATUS COMPLETED Creating a Corresponding Section in the Report 2016-01-26 00:04:55 8.8 STATUS COMPLETED Drawing regional methylation profiles 2016-01-26 00:04:55 8.8 STATUS COMPLETED Exploratory Analysis 2016-01-26 00:04:55 8.8 INFO Initialized report index and saved to index.html 2016-01-26 00:04:55 8.8 STATUS STARTED Differential Methylation 2016-01-26 00:04:55 8.8 INFO Number of cores: 1 2016-01-26 00:04:56 8.8 STATUS STARTED Analysis 2016-01-26 00:04:56 8.8 INFO Using 0 permutation tests 2016-01-26 00:04:56 8.8 INFO Using columns: sampleID,description,filename_bed,tissue,differentiation_level,blood_lineage,cmp_blood_CLP_CMP 2016-01-26 00:04:56 8.8 INFO Using region types: tiling,genes,promoters,cpgislands 2016-01-26 00:04:56 8.8 STATUS STARTED Retrieving comparison info 2016-01-26 00:04:56 8.8 STATUS COMPLETED Retrieving comparison info 2016-01-26 00:04:56 8.8 STATUS STARTED Computing differential methylation tables 2016-01-26 00:04:56 8.8 STATUS STARTED Comparing: B-cell vs. non.B-cell (based on description) 2016-01-26 00:04:56 8.8 STATUS STARTED Computing Differential Methylation Table (Site Level) 2016-01-26 00:04:57 8.8 INFO Conducting differential analysis using limma 2016-01-26 00:07:36 8.6 INFO 2143 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:07:39 8.6 STATUS COMPLETED Computing Differential Methylation Table (Site Level) 2016-01-26 00:07:40 8.6 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2016-01-26 00:12:18 8.5 INFO 112 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:12:19 8.5 STATUS Computed table for tiling 2016-01-26 00:13:15 8.5 INFO 9 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:13:15 8.5 STATUS Computed table for genes 2016-01-26 00:13:51 8.5 INFO 3 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:13:51 8.5 STATUS Computed table for promoters 2016-01-26 00:14:19 8.5 INFO 4 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:14:19 8.5 STATUS Computed table for cpgislands 2016-01-26 00:14:19 8.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2016-01-26 00:14:19 8.5 STATUS COMPLETED Comparing: B-cell vs. non.B-cell (based on description) 2016-01-26 00:14:19 8.5 STATUS STARTED Comparing: Common lymphoid progenitor vs. non.Common lymphoid progenitor (based on description) 2016-01-26 00:14:19 8.5 STATUS STARTED Computing Differential Methylation Table (Site Level) 2016-01-26 00:14:20 8.5 INFO Conducting differential analysis using limma 2016-01-26 00:16:56 8.5 INFO 4527 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:16:59 8.5 STATUS COMPLETED Computing Differential Methylation Table (Site Level) 2016-01-26 00:17:00 8.5 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2016-01-26 00:21:39 8.5 INFO 217 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:21:40 8.5 STATUS Computed table for tiling 2016-01-26 00:22:36 7.5 INFO 8 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:22:36 7.5 STATUS Computed table for genes 2016-01-26 00:23:12 7.5 INFO 19 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:23:12 7.5 STATUS Computed table for promoters 2016-01-26 00:23:40 7.5 INFO 5 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:23:40 7.5 STATUS Computed table for cpgislands 2016-01-26 00:23:40 7.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2016-01-26 00:23:40 7.5 STATUS COMPLETED Comparing: Common lymphoid progenitor vs. non.Common lymphoid progenitor (based on description) 2016-01-26 00:23:40 7.5 STATUS STARTED Comparing: Common myeloid progenitor vs. non.Common myeloid progenitor (based on description) 2016-01-26 00:23:40 7.5 STATUS STARTED Computing Differential Methylation Table (Site Level) 2016-01-26 00:23:41 7.5 INFO Conducting differential analysis using limma 2016-01-26 00:26:16 7.5 INFO 2803 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:26:20 7.5 STATUS COMPLETED Computing Differential Methylation Table (Site Level) 2016-01-26 00:26:21 7.8 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2016-01-26 00:30:59 7.5 INFO 111 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:30:59 7.5 STATUS Computed table for tiling 2016-01-26 00:31:57 7.5 INFO 1 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:31:57 7.5 STATUS Computed table for genes 2016-01-26 00:32:32 7.5 INFO 11 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:32:32 7.5 STATUS Computed table for promoters 2016-01-26 00:33:00 7.5 INFO 8 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:33:00 7.5 STATUS Computed table for cpgislands 2016-01-26 00:33:00 7.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2016-01-26 00:33:00 7.5 STATUS COMPLETED Comparing: Common myeloid progenitor vs. non.Common myeloid progenitor (based on description) 2016-01-26 00:33:00 7.5 STATUS STARTED Comparing: Erythrocyte vs. non.Erythrocyte (based on description) 2016-01-26 00:33:00 7.5 STATUS STARTED Computing Differential Methylation Table (Site Level) 2016-01-26 00:33:01 7.5 INFO Conducting differential analysis using limma 2016-01-26 00:35:38 7.5 INFO 215212 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:35:41 7.5 STATUS COMPLETED Computing Differential Methylation Table (Site Level) 2016-01-26 00:35:42 7.8 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2016-01-26 00:40:18 7.5 INFO 3762 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:40:19 7.5 STATUS Computed table for tiling 2016-01-26 00:41:09 7.5 INFO 137 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:41:09 7.5 STATUS Computed table for genes 2016-01-26 00:41:44 7.5 INFO 201 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:41:44 7.5 STATUS Computed table for promoters 2016-01-26 00:42:12 7.5 INFO 67 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:42:12 7.5 STATUS Computed table for cpgislands 2016-01-26 00:42:12 7.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2016-01-26 00:42:12 7.5 STATUS COMPLETED Comparing: Erythrocyte vs. non.Erythrocyte (based on description) 2016-01-26 00:42:12 7.5 STATUS STARTED Comparing: Hematopoietic stem cell vs. non.Hematopoietic stem cell (based on description) 2016-01-26 00:42:12 7.5 STATUS STARTED Computing Differential Methylation Table (Site Level) 2016-01-26 00:42:13 7.5 INFO Conducting differential analysis using limma 2016-01-26 00:44:49 7.5 INFO 102511 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:44:53 7.5 STATUS COMPLETED Computing Differential Methylation Table (Site Level) 2016-01-26 00:44:54 7.8 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2016-01-26 00:49:27 7.5 INFO 10614 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:49:27 7.5 STATUS Computed table for tiling 2016-01-26 00:50:21 7.5 INFO 429 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:50:21 7.5 STATUS Computed table for genes 2016-01-26 00:50:56 7.5 INFO 574 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:50:56 7.5 STATUS Computed table for promoters 2016-01-26 00:51:24 7.5 INFO 158 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:51:24 7.5 STATUS Computed table for cpgislands 2016-01-26 00:51:24 7.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2016-01-26 00:51:24 7.5 STATUS COMPLETED Comparing: Hematopoietic stem cell vs. non.Hematopoietic stem cell (based on description) 2016-01-26 00:51:24 7.5 STATUS STARTED Comparing: Monocyte vs. non.Monocyte (based on description) 2016-01-26 00:51:24 7.5 STATUS STARTED Computing Differential Methylation Table (Site Level) 2016-01-26 00:51:26 7.5 INFO Conducting differential analysis using limma 2016-01-26 00:54:02 7.5 INFO 215302 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:54:05 7.5 STATUS COMPLETED Computing Differential Methylation Table (Site Level) 2016-01-26 00:54:06 7.8 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2016-01-26 00:58:41 7.5 INFO 3589 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:58:42 7.5 STATUS Computed table for tiling 2016-01-26 00:59:33 7.5 INFO 152 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 00:59:33 7.5 STATUS Computed table for genes 2016-01-26 01:00:07 7.5 INFO 205 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:00:08 7.5 STATUS Computed table for promoters 2016-01-26 01:00:35 7.5 INFO 84 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:00:35 7.5 STATUS Computed table for cpgislands 2016-01-26 01:00:35 7.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2016-01-26 01:00:35 7.5 STATUS COMPLETED Comparing: Monocyte vs. non.Monocyte (based on description) 2016-01-26 01:00:35 7.5 STATUS STARTED Comparing: T helper cell (CD4+) vs. non.T helper cell (CD4+) (based on description) 2016-01-26 01:00:35 7.5 STATUS STARTED Computing Differential Methylation Table (Site Level) 2016-01-26 01:00:36 7.5 INFO Conducting differential analysis using limma 2016-01-26 01:03:11 7.5 INFO 1381 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:03:15 7.5 STATUS COMPLETED Computing Differential Methylation Table (Site Level) 2016-01-26 01:03:16 7.8 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2016-01-26 01:07:55 7.5 INFO 76 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:07:55 7.5 STATUS Computed table for tiling 2016-01-26 01:08:52 7.5 INFO 1 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:08:52 7.5 STATUS Computed table for genes 2016-01-26 01:09:27 7.5 INFO 3 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:09:27 7.5 STATUS Computed table for promoters 2016-01-26 01:09:55 7.5 INFO 1 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:09:55 7.5 STATUS Computed table for cpgislands 2016-01-26 01:09:55 7.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2016-01-26 01:09:55 7.5 STATUS COMPLETED Comparing: T helper cell (CD4+) vs. non.T helper cell (CD4+) (based on description) 2016-01-26 01:09:55 7.5 STATUS STARTED Comparing: differentiated vs. non.differentiated (based on differentiation_level) 2016-01-26 01:09:55 7.5 STATUS STARTED Computing Differential Methylation Table (Site Level) 2016-01-26 01:09:56 7.5 INFO Conducting differential analysis using limma 2016-01-26 01:12:32 7.5 INFO 58 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:12:36 7.5 STATUS COMPLETED Computing Differential Methylation Table (Site Level) 2016-01-26 01:12:37 7.8 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2016-01-26 01:17:16 7.5 INFO 3 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:17:17 7.5 STATUS Computed table for tiling 2016-01-26 01:18:13 7.5 STATUS Computed table for genes 2016-01-26 01:18:48 7.5 STATUS Computed table for promoters 2016-01-26 01:19:16 7.5 STATUS Computed table for cpgislands 2016-01-26 01:19:16 7.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2016-01-26 01:19:17 7.5 STATUS COMPLETED Comparing: differentiated vs. non.differentiated (based on differentiation_level) 2016-01-26 01:19:17 7.5 STATUS STARTED Comparing: progenitor vs. non.progenitor (based on differentiation_level) 2016-01-26 01:19:17 7.5 STATUS STARTED Computing Differential Methylation Table (Site Level) 2016-01-26 01:19:18 7.5 INFO Conducting differential analysis using limma 2016-01-26 01:21:53 7.5 INFO 345 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:21:57 7.5 STATUS COMPLETED Computing Differential Methylation Table (Site Level) 2016-01-26 01:21:57 7.8 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2016-01-26 01:26:37 7.5 INFO 16 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:26:37 7.5 STATUS Computed table for tiling 2016-01-26 01:27:33 7.5 STATUS Computed table for genes 2016-01-26 01:28:09 7.5 STATUS Computed table for promoters 2016-01-26 01:28:37 7.5 STATUS Computed table for cpgislands 2016-01-26 01:28:37 7.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2016-01-26 01:28:37 7.5 STATUS COMPLETED Comparing: progenitor vs. non.progenitor (based on differentiation_level) 2016-01-26 01:28:37 7.5 STATUS STARTED Comparing: stemCell vs. non.stemCell (based on differentiation_level) 2016-01-26 01:28:37 7.5 STATUS STARTED Computing Differential Methylation Table (Site Level) 2016-01-26 01:28:38 7.5 INFO Conducting differential analysis using limma 2016-01-26 01:31:15 7.5 INFO 102511 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:31:18 7.5 STATUS COMPLETED Computing Differential Methylation Table (Site Level) 2016-01-26 01:31:19 7.8 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2016-01-26 01:35:54 7.5 INFO 10614 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:35:54 7.5 STATUS Computed table for tiling 2016-01-26 01:36:47 7.5 INFO 429 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:36:47 7.5 STATUS Computed table for genes 2016-01-26 01:37:23 7.5 INFO 574 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:37:23 7.5 STATUS Computed table for promoters 2016-01-26 01:37:50 7.5 INFO 158 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:37:50 7.5 STATUS Computed table for cpgislands 2016-01-26 01:37:50 7.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2016-01-26 01:37:51 7.5 STATUS COMPLETED Comparing: stemCell vs. non.stemCell (based on differentiation_level) 2016-01-26 01:37:51 7.5 STATUS STARTED Comparing: lymphoid vs. myeloid (based on blood_lineage) 2016-01-26 01:37:51 7.5 STATUS STARTED Computing Differential Methylation Table (Site Level) 2016-01-26 01:37:51 7.5 INFO Conducting differential analysis using limma 2016-01-26 01:40:27 7.5 INFO 341 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:40:30 7.5 STATUS COMPLETED Computing Differential Methylation Table (Site Level) 2016-01-26 01:40:31 7.8 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2016-01-26 01:45:11 7.5 INFO 5 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:45:11 7.5 STATUS Computed table for tiling 2016-01-26 01:46:08 7.5 STATUS Computed table for genes 2016-01-26 01:46:44 7.5 INFO 1 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:46:44 7.5 STATUS Computed table for promoters 2016-01-26 01:47:12 7.5 STATUS Computed table for cpgislands 2016-01-26 01:47:12 7.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2016-01-26 01:47:12 7.5 STATUS COMPLETED Comparing: lymphoid vs. myeloid (based on blood_lineage) 2016-01-26 01:47:12 7.5 STATUS STARTED Comparing: CLP vs. CMP (based on cmp_blood_CLP_CMP) 2016-01-26 01:47:12 7.5 STATUS STARTED Computing Differential Methylation Table (Site Level) 2016-01-26 01:47:13 7.5 INFO Conducting differential analysis using limma 2016-01-26 01:49:41 7.5 INFO 6985 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:49:44 7.5 STATUS COMPLETED Computing Differential Methylation Table (Site Level) 2016-01-26 01:49:45 7.5 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2016-01-26 01:54:24 7.5 INFO 316 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:54:24 7.5 STATUS Computed table for tiling 2016-01-26 01:55:21 7.5 INFO 9 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:55:21 7.5 STATUS Computed table for genes 2016-01-26 01:55:57 7.5 INFO 30 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:55:57 7.5 STATUS Computed table for promoters 2016-01-26 01:56:25 7.5 INFO 13 p-values are NA. They are treated as 1 in FDR adjustment 2016-01-26 01:56:25 7.5 STATUS Computed table for cpgislands 2016-01-26 01:56:25 7.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2016-01-26 01:56:25 7.5 STATUS COMPLETED Comparing: CLP vs. CMP (based on cmp_blood_CLP_CMP) 2016-01-26 01:56:25 7.5 STATUS COMPLETED Computing differential methylation tables 2016-01-26 01:56:25 7.5 INFO Skipping enrichment analysis of differentially methylated regions 2016-01-26 01:56:25 7.5 STATUS COMPLETED Analysis 2016-01-26 01:56:25 7.5 STATUS STARTED Report Generation 2016-01-26 01:56:25 7.5 STATUS Added introductory section 2016-01-26 01:56:25 7.5 STATUS STARTED Adding Site Level Information 2016-01-26 01:56:25 7.5 STATUS STARTED Selection of rank cutoffs 2016-01-26 01:56:42 7.5 STATUS COMPLETED Selection of rank cutoffs 2016-01-26 01:56:42 7.5 STATUS STARTED Adding scatterplots 2016-01-26 05:06:32 12.3 STATUS COMPLETED Adding scatterplots 2016-01-26 05:06:32 12.3 STATUS STARTED Adding volcano plots 2016-01-26 06:19:46 10.2 STATUS COMPLETED Adding volcano plots 2016-01-26 06:19:46 10.2 STATUS STARTED Adding tables 2016-01-26 06:28:54 10.2 STATUS COMPLETED Adding tables 2016-01-26 06:28:54 10.2 STATUS COMPLETED Adding Site Level Information 2016-01-26 06:28:54 10.2 STATUS STARTED Adding Region Level Information 2016-01-26 06:28:54 10.2 STATUS STARTED Selection of rank cutoffs 2016-01-26 06:28:57 10.2 STATUS COMPLETED Selection of rank cutoffs 2016-01-26 06:28:57 10.2 STATUS STARTED Adding scatterplots 2016-01-26 06:34:14 10.6 WARNING Could not assess density colors using densCols: dim(X) must have a positive length 2016-01-26 06:50:38 9.8 WARNING Could not assess density colors using densCols: dim(X) must have a positive length 2016-01-26 06:52:41 9.3 STATUS COMPLETED Adding scatterplots 2016-01-26 06:52:41 9.3 STATUS STARTED Adding volcano plots 2016-01-26 07:07:02 9.3 STATUS COMPLETED Adding volcano plots 2016-01-26 07:07:02 9.3 STATUS STARTED Adding tables 2016-01-26 07:08:03 9.3 STATUS COMPLETED Adding tables 2016-01-26 07:08:03 9.3 STATUS COMPLETED Adding Region Level Information 2016-01-26 07:08:03 9.3 STATUS COMPLETED Report Generation 2016-01-26 07:08:03 9.3 STATUS COMPLETED Differential Methylation 2016-01-26 07:08:03 9.3 INFO Initialized report index and saved to index.html 2016-01-26 07:08:03 9.3 STATUS STARTED Saving RData 2016-01-26 07:10:26 9.3 STATUS COMPLETED Saving RData 2016-01-26 07:10:26 9.3 STATUS COMPLETED RnBeads Pipeline