2016-01-26 11:27:41 0.6 STATUS STARTED RnBeads Pipeline 2016-01-26 11:27:41 0.6 INFO Initialized report index and saved to index.html 2016-01-26 11:27:41 0.6 STATUS STARTED Loading Data 2016-01-26 11:27:41 0.6 INFO Number of cores: 1 2016-01-26 11:27:41 0.6 INFO Loading data of type "infinium.idat.dir" 2016-01-26 11:27:41 0.6 STATUS STARTED Loading Data from IDAT Files 2016-01-26 11:27:41 0.6 INFO Added column barcode to the provided sample annotation table 2016-01-26 11:28:09 1.0 STATUS COMPLETED Loading Data from IDAT Files 2016-01-26 11:29:16 1.3 STATUS Loaded data from /DEEP_fhgfs/projects/RnBeads/tutorial/Epigenomics2016/epigenomics2016/data/Ziller2011_PLoSGen_450K/dataset/idat 2016-01-26 11:29:17 1.3 STATUS Predicted gender for the loaded samples 2016-01-26 11:29:18 1.4 STATUS Added data loading section to the report 2016-01-26 11:29:18 1.4 STATUS Loaded 12 samples and 485577 sites 2016-01-26 11:29:18 1.4 INFO Output object is of type RnBeadRawSet 2016-01-26 11:29:18 1.4 STATUS COMPLETED Loading Data 2016-01-26 11:29:42 1.4 INFO Initialized report index and saved to index.html 2016-01-26 11:29:42 1.4 STATUS STARTED Quality Control 2016-01-26 11:29:42 1.4 INFO Number of cores: 1 2016-01-26 11:29:43 1.4 STATUS STARTED Quality Control Section 2016-01-26 11:30:08 1.2 STATUS Added quality control box plots 2016-01-26 11:32:18 1.2 STATUS Added quality control bar plots 2016-01-26 11:32:21 1.2 STATUS Added negative control boxplots 2016-01-26 11:32:21 1.2 STATUS COMPLETED Quality Control Section 2016-01-26 11:32:21 1.2 STATUS STARTED Visualizing Sample Mixups 2016-01-26 11:32:21 1.2 STATUS STARTED Mixups Visualization Section 2016-01-26 11:32:26 1.3 STATUS Added SNP Heatmap 2016-01-26 11:32:28 1.2 STATUS Calculated Manhattan distances between samples based on SNP probes 2016-01-26 11:32:29 1.2 STATUS Add plot of SNP distances 2016-01-26 11:32:29 1.2 STATUS Exported SNP-based distances to snp_distances.csv 2016-01-26 11:32:29 1.2 STATUS Added SNP-based Distances 2016-01-26 11:32:29 1.2 STATUS COMPLETED Mixups Visualization Section 2016-01-26 11:32:29 1.2 STATUS COMPLETED Visualizing Sample Mixups 2016-01-26 11:32:34 1.3 STATUS COMPLETED Quality Control 2016-01-26 11:32:34 1.3 INFO Initialized report index and saved to index.html 2016-01-26 11:32:34 1.3 STATUS STARTED Preprocessing 2016-01-26 11:32:34 1.3 INFO Number of cores: 1 2016-01-26 11:32:35 1.3 STATUS STARTED Filtering Procedures I 2016-01-26 11:32:36 1.3 STATUS STARTED Removal of SNP-enriched Sites 2016-01-26 11:32:36 1.3 STATUS Removed 4823 sites using SNP criterion "3" 2016-01-26 11:32:36 1.3 STATUS Saved removed sites to /DEEP_fhgfs/projects/RnBeads/tutorial/Epigenomics2016/epigenomics2016/results/report_Ziller2011_vanilla/preprocessing_data/removed_sites_snp.csv 2016-01-26 11:32:36 1.3 STATUS Added a corresponding section to the report 2016-01-26 11:32:36 1.3 STATUS COMPLETED Removal of SNP-enriched Sites 2016-01-26 11:32:37 1.3 INFO Working with a p-value threshold of 0.05 2016-01-26 11:32:37 1.3 STATUS STARTED Greedycut 2016-01-26 11:32:45 1.3 STATUS Calculated a total of 782 iterations 2016-01-26 11:32:45 1.3 INFO Optimal number of iterations is 782 2016-01-26 11:32:48 1.3 STATUS Created ROC plot 2016-01-26 11:32:52 1.3 STATUS Created line plots for matrix dimensions and other statistics 2016-01-26 11:32:52 1.3 STATUS Saved removed sites to /DEEP_fhgfs/projects/RnBeads/tutorial/Epigenomics2016/epigenomics2016/results/report_Ziller2011_vanilla/preprocessing_data/removed_sites_greedycut.csv 2016-01-26 11:32:52 1.3 STATUS COMPLETED Greedycut 2016-01-26 11:32:52 1.3 STATUS Retained 12 samples and 479973 sites 2016-01-26 11:32:52 1.3 STATUS COMPLETED Filtering Procedures I 2016-01-26 11:32:52 1.3 STATUS STARTED Summary of Filtering Procedures I 2016-01-26 11:32:52 1.3 STATUS Creating summary table of removed sites, samples and unreliable measurements... 2016-01-26 11:32:54 1.2 STATUS Saving table and figures... 2016-01-26 11:32:55 1.2 STATUS Added summary table of removed and retained items 2016-01-26 11:32:56 1.4 STATUS Constructed sequences of removed and retained methylation values 2016-01-26 11:33:03 1.3 STATUS Added comparison between removed and retained beta values 2016-01-26 11:33:03 1.3 STATUS COMPLETED Summary of Filtering Procedures I 2016-01-26 11:33:03 1.3 STATUS STARTED Manipulating the object 2016-01-26 11:34:00 1.3 STATUS Removed 5604 sites (probes) 2016-01-26 11:34:00 1.3 STATUS COMPLETED Manipulating the object 2016-01-26 11:34:00 1.3 STATUS STARTED Normalization Procedure 2016-01-26 11:35:30 1.9 STATUS Performed background subtraction with method methylumi.noob 2016-01-26 11:37:04 1.9 STATUS Performed normalization with method "swan" 2016-01-26 11:37:15 2.3 STATUS Added comparison between non-normalized and normalized beta values 2016-01-26 11:37:16 2.4 STATUS Added histogram of observed beta shifts (magnitude of correction) 2016-01-26 11:37:18 2.4 STATUS Added 2D histogram of observed beta values and shifts 2016-01-26 11:37:20 2.4 STATUS Added normalization section 2016-01-26 11:37:20 2.4 STATUS COMPLETED Normalization Procedure 2016-01-26 11:37:20 2.4 STATUS STARTED Filtering Procedures II 2016-01-26 11:37:21 2.4 STATUS STARTED Probe Context Removal 2016-01-26 11:37:21 2.4 STATUS Removed 3146 probe(s) having not acceptable context 2016-01-26 11:37:21 2.4 STATUS Saved removed sites to /DEEP_fhgfs/projects/RnBeads/tutorial/Epigenomics2016/epigenomics2016/results/report_Ziller2011_vanilla/preprocessing_data/removed_sites_context.csv 2016-01-26 11:37:21 2.4 STATUS Added a corresponding section to the report 2016-01-26 11:37:21 2.4 STATUS COMPLETED Probe Context Removal 2016-01-26 11:37:21 2.4 STATUS STARTED Removal of Sites on Sex Chromosomes 2016-01-26 11:37:21 2.4 STATUS Removed 11165 site(s) on sex chromosomes 2016-01-26 11:37:21 2.4 STATUS Saved removed sites to /DEEP_fhgfs/projects/RnBeads/tutorial/Epigenomics2016/epigenomics2016/results/report_Ziller2011_vanilla/preprocessing_data/removed_sites_sex.csv 2016-01-26 11:37:21 2.4 STATUS Added a corresponding section to the report 2016-01-26 11:37:21 2.4 STATUS COMPLETED Removal of Sites on Sex Chromosomes 2016-01-26 11:37:21 2.4 STATUS Retained 12 samples and 465662 sites 2016-01-26 11:37:21 2.4 STATUS COMPLETED Filtering Procedures II 2016-01-26 11:37:21 2.4 STATUS STARTED Summary of Filtering Procedures II 2016-01-26 11:37:21 2.4 STATUS Creating summary table of removed sites, samples and unreliable measurements... 2016-01-26 11:37:22 2.5 STATUS Saving table and figures... 2016-01-26 11:37:23 2.5 STATUS Added summary table of removed and retained items 2016-01-26 11:37:24 2.4 STATUS Constructed sequences of removed and retained methylation values 2016-01-26 11:37:31 2.0 STATUS Added comparison between removed and retained beta values 2016-01-26 11:37:31 2.0 STATUS COMPLETED Summary of Filtering Procedures II 2016-01-26 11:37:31 2.0 STATUS STARTED Manipulating the object 2016-01-26 11:38:32 2.0 STATUS Removed 14311 sites (probes) 2016-01-26 11:38:32 2.0 STATUS COMPLETED Manipulating the object 2016-01-26 11:38:32 2.0 STATUS COMPLETED Preprocessing 2016-01-26 11:38:53 2.0 INFO Initialized report index and saved to index.html 2016-01-26 11:38:53 2.0 STATUS STARTED Tracks and Tables 2016-01-26 11:38:53 2.0 INFO Number of cores: 1 2016-01-26 11:38:53 2.0 STATUS STARTED Generating Tracks and Tables 2016-01-26 11:38:53 2.0 STATUS STARTED Exporting sites 2016-01-26 11:38:53 2.0 STATUS STARTED Creating Track Hub -- bigBed 2016-01-26 11:38:53 2.0 STATUS STARTED Conversion to BED 2016-01-26 11:38:53 2.0 STATUS Converting to GRangesList 2016-01-26 11:38:58 2.0 STATUS Exporting sample hES_HUES13_p47 2016-01-26 11:39:02 2.0 STATUS Exporting sample hiPS_20b_p43 2016-01-26 11:39:06 2.0 STATUS Exporting sample hES_HUES1_p29 2016-01-26 11:39:09 2.0 STATUS Exporting sample hiPS_11c_p23 2016-01-26 11:39:13 2.0 STATUS Exporting sample hES_HUES1_p28 2016-01-26 11:39:17 2.0 STATUS Exporting sample hiPS_20b_p49_TeSR 2016-01-26 11:39:21 2.0 STATUS Exporting sample hiPS_20b_p49_KOSR 2016-01-26 11:39:25 2.0 STATUS Exporting sample hiPS_17b_p35_TeSR 2016-01-26 11:39:29 2.0 STATUS Exporting sample hiPS_27b_p31 2016-01-26 11:39:33 2.0 STATUS Exporting sample hES_HUES64_p19 2016-01-26 11:39:36 2.0 STATUS Exporting sample hiPS_17b_p35_KOSR 2016-01-26 11:39:40 2.0 STATUS Exporting sample hES_H9_p58 2016-01-26 11:39:44 2.0 STATUS COMPLETED Conversion to BED 2016-01-26 11:39:44 2.0 STATUS STARTED Creating Track Hub 2016-01-26 11:40:17 2.0 STATUS COMPLETED Creating Track Hub 2016-01-26 11:40:17 2.0 STATUS COMPLETED Creating Track Hub -- bigBed 2016-01-26 11:40:17 2.0 STATUS STARTED Creating UCSC Track Hub -- bigWig 2016-01-26 11:40:17 2.0 STATUS STARTED Conversion to bedGraph 2016-01-26 11:40:36 2.0 STATUS COMPLETED Conversion to bedGraph 2016-01-26 11:40:36 2.0 STATUS STARTED Creating Track Hub 2016-01-26 11:40:52 2.0 STATUS COMPLETED Creating Track Hub 2016-01-26 11:40:52 2.0 STATUS COMPLETED Creating UCSC Track Hub -- bigWig 2016-01-26 11:40:52 2.0 STATUS COMPLETED Exporting sites 2016-01-26 11:40:52 2.0 STATUS COMPLETED Generating Tracks and Tables 2016-01-26 11:40:52 2.0 STATUS STARTED Writing export report 2016-01-26 11:41:07 2.0 STATUS COMPLETED Writing export report 2016-01-26 11:41:07 2.0 STATUS COMPLETED Tracks and Tables 2016-01-26 11:41:07 2.0 INFO Initialized report index and saved to index.html 2016-01-26 11:41:08 2.0 STATUS STARTED Exploratory Analysis 2016-01-26 11:41:08 2.0 INFO Number of cores: 1 2016-01-26 11:41:08 2.0 STATUS Designed color mappings for probe type and CGI status 2016-01-26 11:41:30 2.0 STATUS STARTED Dimension Reduction Techniques 2016-01-26 11:41:31 2.1 STATUS STARTED MDS 2016-01-26 11:41:32 2.1 STATUS Calculated MDS coordinates using manhattan distance 2016-01-26 11:41:32 2.1 STATUS Calculated MDS coordinates using euclidean distance 2016-01-26 11:41:32 2.1 STATUS COMPLETED MDS 2016-01-26 11:41:32 2.1 STATUS STARTED PCA 2016-01-26 11:41:32 2.1 INFO Removed 22 loci ( sites ) because they contain missing values 2016-01-26 11:41:33 2.1 STATUS COMPLETED PCA 2016-01-26 11:41:33 2.1 STATUS STARTED MDS 2016-01-26 11:41:33 2.1 STATUS Calculated MDS coordinates using manhattan distance 2016-01-26 11:41:33 2.1 STATUS Calculated MDS coordinates using euclidean distance 2016-01-26 11:41:33 2.1 STATUS COMPLETED MDS 2016-01-26 11:41:33 2.1 STATUS STARTED PCA 2016-01-26 11:41:34 2.1 INFO Removed 1 loci ( tiling ) because they contain missing values 2016-01-26 11:41:34 2.1 STATUS COMPLETED PCA 2016-01-26 11:41:34 2.1 STATUS STARTED MDS 2016-01-26 11:41:34 2.1 STATUS Calculated MDS coordinates using manhattan distance 2016-01-26 11:41:34 2.1 STATUS Calculated MDS coordinates using euclidean distance 2016-01-26 11:41:34 2.1 STATUS COMPLETED MDS 2016-01-26 11:41:34 2.1 STATUS STARTED PCA 2016-01-26 11:41:34 2.1 STATUS COMPLETED PCA 2016-01-26 11:41:34 2.1 STATUS STARTED MDS 2016-01-26 11:41:34 2.1 STATUS Calculated MDS coordinates using manhattan distance 2016-01-26 11:41:34 2.1 STATUS Calculated MDS coordinates using euclidean distance 2016-01-26 11:41:34 2.1 STATUS COMPLETED MDS 2016-01-26 11:41:34 2.1 STATUS STARTED PCA 2016-01-26 11:41:34 2.1 STATUS COMPLETED PCA 2016-01-26 11:41:34 2.1 STATUS STARTED MDS 2016-01-26 11:41:34 2.1 STATUS Calculated MDS coordinates using manhattan distance 2016-01-26 11:41:34 2.1 STATUS Calculated MDS coordinates using euclidean distance 2016-01-26 11:41:34 2.1 STATUS COMPLETED MDS 2016-01-26 11:41:34 2.1 STATUS STARTED PCA 2016-01-26 11:41:34 2.1 INFO Removed 1 loci ( cpgislands ) because they contain missing values 2016-01-26 11:41:34 2.1 STATUS COMPLETED PCA 2016-01-26 11:41:34 2.1 INFO Mapping 4 traits to point colors and types 2016-01-26 11:52:49 2.0 INFO Principal components that explain at least 95 % of the total variance: 9 2016-01-26 11:52:49 2.0 INFO Saved percentage of total variance to pca_variance_explained_1.csv 2016-01-26 11:52:50 2.0 INFO Principal components that explain at least 95 % of the total variance: 9 2016-01-26 11:52:50 2.0 INFO Saved percentage of total variance to pca_variance_explained_2.csv 2016-01-26 11:52:51 2.0 INFO Principal components that explain at least 95 % of the total variance: 8 2016-01-26 11:52:51 2.0 INFO Saved percentage of total variance to pca_variance_explained_3.csv 2016-01-26 11:52:52 2.0 INFO Principal components that explain at least 95 % of the total variance: 8 2016-01-26 11:52:52 2.0 INFO Saved percentage of total variance to pca_variance_explained_4.csv 2016-01-26 11:52:53 2.0 INFO Principal components that explain at least 95 % of the total variance: 8 2016-01-26 11:52:53 2.0 INFO Saved percentage of total variance to pca_variance_explained_5.csv 2016-01-26 11:52:54 2.0 STATUS Created scatter plots and CDFs summarizing the reduced dimensional representations 2016-01-26 11:52:54 2.0 STATUS COMPLETED Dimension Reduction Techniques 2016-01-26 11:52:54 2.0 STATUS STARTED Tests for Associations 2016-01-26 11:52:55 2.0 INFO Testing the following traits for associations: Sample_Group; Cell_Line; Passage_No; Treatment; CellType; Predicted Male Probability; Predicted Gender 2016-01-26 11:52:55 2.0 STATUS Created 10000 sample permutations 2016-01-26 11:54:01 2.0 STATUS Computed correlations between principal components and traits. 2016-01-26 11:54:02 2.0 STATUS Computed pairwise correlations between traits. 2016-01-26 11:54:02 2.0 STATUS COMPLETED Tests for Associations 2016-01-26 11:54:17 2.0 STATUS STARTED Quality-associated Batch Effects 2016-01-26 11:56:59 2.0 STATUS Computed associations between 8 principal component(s) and bisulfite conversion I for sites 2016-01-26 11:57:53 2.0 STATUS Computed associations between 8 principal component(s) and bisulfite conversion II for sites 2016-01-26 11:58:47 2.0 STATUS Computed associations between 8 principal component(s) and extension for sites 2016-01-26 11:59:27 2.0 STATUS Computed associations between 8 principal component(s) and hybridization for sites 2016-01-26 12:00:21 2.0 STATUS Computed associations between 8 principal component(s) and non-polymorphic for sites 2016-01-26 12:03:01 2.0 STATUS Computed associations between 8 principal component(s) and specificity I for sites 2016-01-26 12:03:42 2.0 STATUS Computed associations between 8 principal component(s) and specificity II for sites 2016-01-26 12:04:35 2.0 STATUS Computed associations between 8 principal component(s) and staining for sites 2016-01-26 12:05:02 2.0 STATUS Computed associations between 8 principal component(s) and target removal for sites 2016-01-26 12:07:43 2.0 STATUS Computed associations between 8 principal component(s) and bisulfite conversion I for tiling 2016-01-26 12:08:37 2.0 STATUS Computed associations between 8 principal component(s) and bisulfite conversion II for tiling 2016-01-26 12:09:30 2.0 STATUS Computed associations between 8 principal component(s) and extension for tiling 2016-01-26 12:10:10 2.0 STATUS Computed associations between 8 principal component(s) and hybridization for tiling 2016-01-26 12:11:05 2.0 STATUS Computed associations between 8 principal component(s) and non-polymorphic for tiling 2016-01-26 12:13:45 2.0 STATUS Computed associations between 8 principal component(s) and specificity I for tiling 2016-01-26 12:14:25 2.0 STATUS Computed associations between 8 principal component(s) and specificity II for tiling 2016-01-26 12:15:19 2.0 STATUS Computed associations between 8 principal component(s) and staining for tiling 2016-01-26 12:15:46 2.0 STATUS Computed associations between 8 principal component(s) and target removal for tiling 2016-01-26 12:18:27 2.0 STATUS Computed associations between 8 principal component(s) and bisulfite conversion I for genes 2016-01-26 12:19:20 2.0 STATUS Computed associations between 8 principal component(s) and bisulfite conversion II for genes 2016-01-26 12:20:14 2.0 STATUS Computed associations between 8 principal component(s) and extension for genes 2016-01-26 12:20:54 2.0 STATUS Computed associations between 8 principal component(s) and hybridization for genes 2016-01-26 12:21:48 2.0 STATUS Computed associations between 8 principal component(s) and non-polymorphic for genes 2016-01-26 12:24:29 2.0 STATUS Computed associations between 8 principal component(s) and specificity I for genes 2016-01-26 12:25:09 2.0 STATUS Computed associations between 8 principal component(s) and specificity II for genes 2016-01-26 12:26:03 2.0 STATUS Computed associations between 8 principal component(s) and staining for genes 2016-01-26 12:26:29 2.0 STATUS Computed associations between 8 principal component(s) and target removal for genes 2016-01-26 12:29:10 2.0 STATUS Computed associations between 8 principal component(s) and bisulfite conversion I for promoters 2016-01-26 12:30:04 2.0 STATUS Computed associations between 8 principal component(s) and bisulfite conversion II for promoters 2016-01-26 12:30:58 2.0 STATUS Computed associations between 8 principal component(s) and extension for promoters 2016-01-26 12:31:38 2.0 STATUS Computed associations between 8 principal component(s) and hybridization for promoters 2016-01-26 12:32:31 2.0 STATUS Computed associations between 8 principal component(s) and non-polymorphic for promoters 2016-01-26 12:35:13 2.0 STATUS Computed associations between 8 principal component(s) and specificity I for promoters 2016-01-26 12:35:54 2.0 STATUS Computed associations between 8 principal component(s) and specificity II for promoters 2016-01-26 12:36:47 2.0 STATUS Computed associations between 8 principal component(s) and staining for promoters 2016-01-26 12:37:15 2.0 STATUS Computed associations between 8 principal component(s) and target removal for promoters 2016-01-26 12:39:55 2.0 STATUS Computed associations between 8 principal component(s) and bisulfite conversion I for cpgislands 2016-01-26 12:40:49 2.0 STATUS Computed associations between 8 principal component(s) and bisulfite conversion II for cpgislands 2016-01-26 12:41:42 2.0 STATUS Computed associations between 8 principal component(s) and extension for cpgislands 2016-01-26 12:42:23 2.0 STATUS Computed associations between 8 principal component(s) and hybridization for cpgislands 2016-01-26 12:43:16 2.0 STATUS Computed associations between 8 principal component(s) and non-polymorphic for cpgislands 2016-01-26 12:45:58 2.0 STATUS Computed associations between 8 principal component(s) and specificity I for cpgislands 2016-01-26 12:46:38 2.0 STATUS Computed associations between 8 principal component(s) and specificity II for cpgislands 2016-01-26 12:47:32 2.0 STATUS Computed associations between 8 principal component(s) and staining for cpgislands 2016-01-26 12:47:59 2.0 STATUS Computed associations between 8 principal component(s) and target removal for cpgislands 2016-01-26 12:51:11 2.0 STATUS Added heatmaps of correlation between principal components and signal levels of Q probes 2016-01-26 12:51:11 2.0 STATUS COMPLETED Quality-associated Batch Effects 2016-01-26 12:51:13 2.0 STATUS STARTED Methylation Value Distributions - Sample Groups 2016-01-26 12:51:13 2.0 INFO processing beta_density_samples_1_1 2016-01-26 12:51:14 2.0 INFO Density estimation ( all samples--sites ): Groupwise retained observations after missing value removal: all:5587922/5587944 2016-01-26 12:51:14 2.0 INFO Density estimation ( all samples--sites ): Groupwise retained observations after subsampling: all:1000000/5587922 2016-01-26 12:51:17 2.0 INFO processing beta_density_samples_1_2 2016-01-26 12:51:17 2.0 INFO Density estimation ( all samples--tiling ): Groupwise retained observations after missing value removal: all:1589819/1589820 2016-01-26 12:51:17 2.0 INFO Density estimation ( all samples--tiling ): Groupwise retained observations after subsampling: all:1000000/1589819 2016-01-26 12:51:21 2.0 INFO processing beta_density_samples_1_3 2016-01-26 12:51:21 2.0 INFO Density estimation ( all samples--genes ): Groupwise retained observations after missing value removal: all:357948/357948 2016-01-26 12:51:22 2.0 INFO processing beta_density_samples_1_4 2016-01-26 12:51:22 2.0 INFO Density estimation ( all samples--promoters ): Groupwise retained observations after missing value removal: all:360060/360060 2016-01-26 12:51:24 2.0 INFO processing beta_density_samples_1_5 2016-01-26 12:51:24 2.0 INFO Density estimation ( all samples--cpgislands ): Groupwise retained observations after missing value removal: all:310235/310236 2016-01-26 12:51:25 2.0 INFO processing beta_density_samples_2_1 2016-01-26 12:51:25 2.0 INFO Density estimation ( Sample_Group--sites ): Groupwise retained observations after missing value removal: hESC:2328306/2328310; hiPSC:3259616/3259634 2016-01-26 12:51:26 2.0 INFO Density estimation ( Sample_Group--sites ): Groupwise retained observations after subsampling: hESC:833335/2328306; hiPSC:1166665/3259616 2016-01-26 12:51:35 2.1 INFO processing beta_density_samples_2_2 2016-01-26 12:51:35 2.1 INFO Density estimation ( Sample_Group--tiling ): Groupwise retained observations after missing value removal: hESC:662425/662425; hiPSC:927394/927395 2016-01-26 12:51:42 2.1 INFO processing beta_density_samples_2_3 2016-01-26 12:51:42 2.1 INFO Density estimation ( Sample_Group--genes ): Groupwise retained observations after missing value removal: hESC:149145/149145; hiPSC:208803/208803 2016-01-26 12:51:44 2.1 INFO processing beta_density_samples_2_4 2016-01-26 12:51:44 2.1 INFO Density estimation ( Sample_Group--promoters ): Groupwise retained observations after missing value removal: hESC:150025/150025; hiPSC:210035/210035 2016-01-26 12:51:46 2.1 INFO processing beta_density_samples_2_5 2016-01-26 12:51:46 2.1 INFO Density estimation ( Sample_Group--cpgislands ): Groupwise retained observations after missing value removal: hESC:129265/129265; hiPSC:180970/180971 2016-01-26 12:51:47 2.1 INFO processing beta_density_samples_3_1 2016-01-26 12:51:48 2.1 INFO Density estimation ( Treatment--sites ): Groupwise retained observations after missing value removal: KOSR:931322/931324; TeSR:931322/931324 2016-01-26 12:51:56 2.1 INFO processing beta_density_samples_3_2 2016-01-26 12:51:57 2.1 INFO Density estimation ( Treatment--tiling ): Groupwise retained observations after missing value removal: KOSR:264970/264970; TeSR:264970/264970 2016-01-26 12:51:59 2.1 INFO processing beta_density_samples_3_3 2016-01-26 12:51:59 2.1 INFO Density estimation ( Treatment--genes ): Groupwise retained observations after missing value removal: KOSR:59658/59658; TeSR:59658/59658 2016-01-26 12:52:00 2.1 INFO processing beta_density_samples_3_4 2016-01-26 12:52:00 2.1 INFO Density estimation ( Treatment--promoters ): Groupwise retained observations after missing value removal: KOSR:60010/60010; TeSR:60010/60010 2016-01-26 12:52:01 2.1 INFO processing beta_density_samples_3_5 2016-01-26 12:52:01 2.1 INFO Density estimation ( Treatment--cpgislands ): Groupwise retained observations after missing value removal: KOSR:51706/51706; TeSR:51706/51706 2016-01-26 12:52:02 2.1 INFO processing beta_density_samples_4_1 2016-01-26 12:52:03 2.1 INFO Density estimation ( CellType--sites ): Groupwise retained observations after missing value removal: CT1:931321/931324; CT2:931310/931324 2016-01-26 12:52:11 2.1 INFO processing beta_density_samples_4_2 2016-01-26 12:52:11 2.1 INFO Density estimation ( CellType--tiling ): Groupwise retained observations after missing value removal: CT1:264970/264970; CT2:264969/264970 2016-01-26 12:52:14 2.1 INFO processing beta_density_samples_4_3 2016-01-26 12:52:14 2.1 INFO Density estimation ( CellType--genes ): Groupwise retained observations after missing value removal: CT1:59658/59658; CT2:59658/59658 2016-01-26 12:52:15 2.1 INFO processing beta_density_samples_4_4 2016-01-26 12:52:15 2.1 INFO Density estimation ( CellType--promoters ): Groupwise retained observations after missing value removal: CT1:60010/60010; CT2:60010/60010 2016-01-26 12:52:16 2.1 INFO processing beta_density_samples_4_5 2016-01-26 12:52:16 2.1 INFO Density estimation ( CellType--cpgislands ): Groupwise retained observations after missing value removal: CT1:51706/51706; CT2:51705/51706 2016-01-26 12:52:18 2.1 INFO processing beta_density_samples_5_1 2016-01-26 12:52:18 2.1 INFO Density estimation ( Predicted Gender--sites ): Groupwise retained observations after missing value removal: female:2793968/2793972; male:2793954/2793972 2016-01-26 12:52:18 2.1 INFO Density estimation ( Predicted Gender--sites ): Groupwise retained observations after subsampling: female:1000003/2793968; male:999997/2793954 2016-01-26 12:52:27 2.1 INFO processing beta_density_samples_5_2 2016-01-26 12:52:27 2.1 INFO Density estimation ( Predicted Gender--tiling ): Groupwise retained observations after missing value removal: female:794910/794910; male:794909/794910 2016-01-26 12:52:35 2.0 INFO processing beta_density_samples_5_3 2016-01-26 12:52:35 2.0 INFO Density estimation ( Predicted Gender--genes ): Groupwise retained observations after missing value removal: female:178974/178974; male:178974/178974 2016-01-26 12:52:37 2.0 INFO processing beta_density_samples_5_4 2016-01-26 12:52:37 2.0 INFO Density estimation ( Predicted Gender--promoters ): Groupwise retained observations after missing value removal: female:180030/180030; male:180030/180030 2016-01-26 12:52:39 2.0 INFO processing beta_density_samples_5_5 2016-01-26 12:52:39 2.0 INFO Density estimation ( Predicted Gender--cpgislands ): Groupwise retained observations after missing value removal: female:155118/155118; male:155117/155118 2016-01-26 12:52:41 2.0 STATUS COMPLETED Methylation Value Distributions - Sample Groups 2016-01-26 12:52:41 2.0 STATUS STARTED Methylation Value Distributions - Probe Categories 2016-01-26 12:52:42 2.0 INFO Density estimation ( CGI Relation--all samples ): Groupwise retained observations after missing value removal: Open Sea:2014998/2015004; Shelf:541788/541788; Shore:1295381/1295388; Island:1735755/1735764 2016-01-26 12:52:42 2.0 INFO Density estimation ( CGI Relation--all samples ): Groupwise retained observations after subsampling: Open Sea:1442395/2014998; Shelf:387828/541788; Shore:927272/1295381; Island:1242505/1735755 2016-01-26 12:52:59 2.5 INFO Density estimation ( Design--all samples ): Groupwise retained observations after missing value removal: I:1571848/1571856; II:4016074/4016088 2016-01-26 12:53:00 2.5 INFO Density estimation ( Design--all samples ): Groupwise retained observations after subsampling: I:562588/1571848; II:1437412/4016074 2016-01-26 12:53:07 2.4 INFO Density estimation ( CGI Relation--hESC (based on Sample_Group) ): Groupwise retained observations after missing value removal: Open Sea:839584/839585; Shelf:225745/225745; Shore:539745/539745; Island:723232/723235 2016-01-26 12:53:15 2.4 INFO Density estimation ( Design--hESC (based on Sample_Group) ): Groupwise retained observations after missing value removal: I:654936/654940; II:1673370/1673370 2016-01-26 12:53:16 2.4 INFO Density estimation ( Design--hESC (based on Sample_Group) ): Groupwise retained observations after subsampling: I:562586/654936; II:1437414/1673370 2016-01-26 12:53:23 2.4 INFO Density estimation ( CGI Relation--hiPSC (based on Sample_Group) ): Groupwise retained observations after missing value removal: Open Sea:1175414/1175419; Shelf:316043/316043; Shore:755636/755643; Island:1012523/1012529 2016-01-26 12:53:35 2.5 INFO Density estimation ( Design--hiPSC (based on Sample_Group) ): Groupwise retained observations after missing value removal: I:916912/916916; II:2342704/2342718 2016-01-26 12:53:35 2.5 INFO Density estimation ( Design--hiPSC (based on Sample_Group) ): Groupwise retained observations after subsampling: I:562589/916912; II:1437411/2342704 2016-01-26 12:53:42 2.4 INFO Density estimation ( CGI Relation--KOSR (based on Treatment) ): Groupwise retained observations after missing value removal: Open Sea:335832/335834; Shelf:90298/90298; Shore:215898/215898; Island:289294/289294 2016-01-26 12:53:46 2.4 INFO Density estimation ( Design--KOSR (based on Treatment) ): Groupwise retained observations after missing value removal: I:261974/261976; II:669348/669348 2016-01-26 12:53:50 2.1 INFO Density estimation ( CGI Relation--TeSR (based on Treatment) ): Groupwise retained observations after missing value removal: Open Sea:335834/335834; Shelf:90298/90298; Shore:215898/215898; Island:289292/289294 2016-01-26 12:53:53 2.2 INFO Density estimation ( Design--TeSR (based on Treatment) ): Groupwise retained observations after missing value removal: I:261974/261976; II:669348/669348 2016-01-26 12:53:57 2.2 INFO Density estimation ( CGI Relation--CT1 (based on CellType) ): Groupwise retained observations after missing value removal: Open Sea:335833/335834; Shelf:90298/90298; Shore:215898/215898; Island:289292/289294 2016-01-26 12:54:00 2.2 INFO Density estimation ( Design--CT1 (based on CellType) ): Groupwise retained observations after missing value removal: I:261973/261976; II:669348/669348 2016-01-26 12:54:04 2.0 INFO Density estimation ( CGI Relation--CT2 (based on CellType) ): Groupwise retained observations after missing value removal: Open Sea:335831/335834; Shelf:90298/90298; Shore:215891/215898; Island:289290/289294 2016-01-26 12:54:08 2.2 INFO Density estimation ( Design--CT2 (based on CellType) ): Groupwise retained observations after missing value removal: I:261976/261976; II:669334/669348 2016-01-26 12:54:11 2.2 INFO Density estimation ( CGI Relation--female (based on Predicted Gender) ): Groupwise retained observations after missing value removal: Open Sea:1007500/1007502; Shelf:270894/270894; Shore:647694/647694; Island:867880/867882 2016-01-26 12:54:21 2.4 INFO Density estimation ( Design--female (based on Predicted Gender) ): Groupwise retained observations after missing value removal: I:785924/785928; II:2008044/2008044 2016-01-26 12:54:21 2.4 INFO Density estimation ( Design--female (based on Predicted Gender) ): Groupwise retained observations after subsampling: I:562586/785924; II:1437414/2008044 2016-01-26 12:54:28 2.3 INFO Density estimation ( CGI Relation--male (based on Predicted Gender) ): Groupwise retained observations after missing value removal: Open Sea:1007498/1007502; Shelf:270894/270894; Shore:647687/647694; Island:867875/867882 2016-01-26 12:54:39 2.4 INFO Density estimation ( Design--male (based on Predicted Gender) ): Groupwise retained observations after missing value removal: I:785924/785928; II:2008030/2008044 2016-01-26 12:54:39 2.4 INFO Density estimation ( Design--male (based on Predicted Gender) ): Groupwise retained observations after subsampling: I:562589/785924; II:1437411/2008030 2016-01-26 12:54:46 2.4 STATUS COMPLETED Methylation Value Distributions - Probe Categories 2016-01-26 12:54:46 2.2 STATUS STARTED Scatter Plots of Mean Beta vs Variance 2016-01-26 12:54:46 2.2 INFO Sample subgroups are defined by: Sample_Group; Treatment; CellType; Predicted Gender 2016-01-26 13:14:36 2.2 WARNING Removed 2 loci with missing values in group KOSR (based on Treatment) 2016-01-26 13:21:12 2.2 WARNING Removed 2 loci with missing values in group TeSR (based on Treatment) 2016-01-26 13:27:49 2.2 WARNING Removed 3 loci with missing values in group CT1 (based on CellType) 2016-01-26 13:34:27 2.2 WARNING Removed 14 loci with missing values in group CT2 (based on CellType) 2016-01-26 13:54:22 2.3 STATUS Created 36 scatter plots of methylation variance on the site level 2016-01-26 14:00:16 2.2 WARNING Removed 1 loci with missing values in group CT2 (based on CellType) 2016-01-26 14:09:15 2.0 WARNING Removed 1 loci with missing values in group CT2 (based on CellType) 2016-01-26 14:09:56 2.0 STATUS Created 72 scatter plots of methylation variance on the region level 2016-01-26 14:09:56 2.0 STATUS COMPLETED Scatter Plots of Mean Beta vs Variance 2016-01-26 14:09:56 2.0 STATUS STARTED Deviation Plots 2016-01-26 14:23:06 2.0 STATUS Created 27 deviation plots on the site level 2016-01-26 14:26:49 2.0 STATUS Created 36 deviation plots on the region level 2016-01-26 14:26:50 2.0 STATUS Added summary table of variabilities 2016-01-26 14:26:50 2.0 STATUS COMPLETED Deviation Plots 2016-01-26 14:26:50 2.0 STATUS STARTED Sample Clustering 2016-01-26 14:26:50 2.0 STATUS STARTED Agglomerative Hierarchical Clustering 2016-01-26 14:26:52 2.2 STATUS Performed clustering on sites using correlation as a distance metric 2016-01-26 14:26:52 2.2 STATUS Performed clustering on sites using manhattan as a distance metric 2016-01-26 14:26:52 2.2 STATUS Performed clustering on sites using euclidean as a distance metric 2016-01-26 14:26:53 2.2 STATUS Performed clustering on tiling using correlation as a distance metric 2016-01-26 14:26:53 2.2 STATUS Performed clustering on tiling using manhattan as a distance metric 2016-01-26 14:26:53 2.0 STATUS Performed clustering on tiling using euclidean as a distance metric 2016-01-26 14:26:53 2.0 STATUS Performed clustering on genes using correlation as a distance metric 2016-01-26 14:26:53 2.0 STATUS Performed clustering on genes using manhattan as a distance metric 2016-01-26 14:26:53 2.0 STATUS Performed clustering on genes using euclidean as a distance metric 2016-01-26 14:26:53 2.0 STATUS Performed clustering on promoters using correlation as a distance metric 2016-01-26 14:26:53 2.0 STATUS Performed clustering on promoters using manhattan as a distance metric 2016-01-26 14:26:53 2.0 STATUS Performed clustering on promoters using euclidean as a distance metric 2016-01-26 14:26:53 2.0 STATUS Performed clustering on cpgislands using correlation as a distance metric 2016-01-26 14:26:53 2.0 STATUS Performed clustering on cpgislands using manhattan as a distance metric 2016-01-26 14:26:53 2.0 STATUS Performed clustering on cpgislands using euclidean as a distance metric 2016-01-26 14:26:53 2.0 STATUS COMPLETED Agglomerative Hierarchical Clustering 2016-01-26 14:26:54 2.1 STATUS STARTED Clustering Section 2016-01-26 14:26:54 2.1 STATUS STARTED Generating Heatmaps 2016-01-26 14:26:54 2.1 STATUS STARTED Region type: sites 2016-01-26 14:32:13 2.0 STATUS COMPLETED Region type: sites 2016-01-26 14:32:13 2.0 STATUS STARTED Region type: tiling 2016-01-26 14:37:28 2.0 STATUS COMPLETED Region type: tiling 2016-01-26 14:37:28 2.0 STATUS STARTED Region type: genes 2016-01-26 14:42:46 2.0 STATUS COMPLETED Region type: genes 2016-01-26 14:42:46 2.0 STATUS STARTED Region type: promoters 2016-01-26 14:48:03 2.0 STATUS COMPLETED Region type: promoters 2016-01-26 14:48:03 2.0 STATUS STARTED Region type: cpgislands 2016-01-26 14:53:23 2.0 STATUS COMPLETED Region type: cpgislands 2016-01-26 14:53:23 2.0 STATUS Created 720 heatmaps based on the clustering results 2016-01-26 14:53:23 2.0 STATUS COMPLETED Generating Heatmaps 2016-01-26 14:53:23 2.0 STATUS STARTED Adding Color Legends 2016-01-26 14:54:48 2.0 STATUS COMPLETED Adding Color Legends 2016-01-26 14:54:48 2.0 STATUS STARTED Estimating Optimal Numbers of Clusters 2016-01-26 14:55:07 2.0 STATUS Estimated number of clusters based on mean silhouette value 2016-01-26 14:55:07 2.0 STATUS COMPLETED Estimating Optimal Numbers of Clusters 2016-01-26 14:55:07 2.0 STATUS STARTED Overlapping Clusters with Sample Traits 2016-01-26 14:55:07 2.0 STATUS Computed adjusted rand indices and saved to exploratory_analysis_data/adjusted_rand_indices_1.csv 2016-01-26 14:55:07 2.0 STATUS Computed adjusted rand indices and saved to exploratory_analysis_data/adjusted_rand_indices_2.csv 2016-01-26 14:55:07 2.0 STATUS Computed adjusted rand indices and saved to exploratory_analysis_data/adjusted_rand_indices_3.csv 2016-01-26 14:55:07 2.0 STATUS Computed adjusted rand indices and saved to exploratory_analysis_data/adjusted_rand_indices_4.csv 2016-01-26 14:55:07 2.0 STATUS Computed adjusted rand indices and saved to exploratory_analysis_data/adjusted_rand_indices_5.csv 2016-01-26 14:55:24 2.0 STATUS COMPLETED Overlapping Clusters with Sample Traits 2016-01-26 14:55:24 2.0 STATUS COMPLETED Clustering Section 2016-01-26 14:55:24 2.0 STATUS COMPLETED Sample Clustering 2016-01-26 14:55:24 2.0 STATUS STARTED Drawing regional methylation profiles 2016-01-26 14:55:24 2.0 STATUS STARTED Creating a Corresponding Section in the Report 2016-01-26 14:55:27 2.0 STATUS Plotting region profiles for region genes and column all samples ... 2016-01-26 14:58:57 9.4 STATUS Plotting region profiles for region genes and column Sample_Group ... 2016-01-26 15:02:02 8.5 STATUS Plotting region profiles for region genes and column Treatment ... 2016-01-26 15:02:58 7.4 STATUS Plotting region profiles for region genes and column CellType ... 2016-01-26 15:03:55 7.0 STATUS Plotting region profiles for region genes and column Predicted Gender ... 2016-01-26 15:07:01 8.6 STATUS Plotting region profiles for region promoters and column all samples ... 2016-01-26 15:08:01 8.7 STATUS Plotting region profiles for region promoters and column Sample_Group ... 2016-01-26 15:08:59 6.6 STATUS Plotting region profiles for region promoters and column Treatment ... 2016-01-26 15:09:20 6.4 STATUS Plotting region profiles for region promoters and column CellType ... 2016-01-26 15:09:39 6.4 STATUS Plotting region profiles for region promoters and column Predicted Gender ... 2016-01-26 15:10:40 6.4 STATUS Plotting region profiles for region cpgislands and column all samples ... 2016-01-26 15:11:23 6.4 STATUS Plotting region profiles for region cpgislands and column Sample_Group ... 2016-01-26 15:12:07 6.4 STATUS Plotting region profiles for region cpgislands and column Treatment ... 2016-01-26 15:12:21 6.4 STATUS Plotting region profiles for region cpgislands and column CellType ... 2016-01-26 15:12:35 6.4 STATUS Plotting region profiles for region cpgislands and column Predicted Gender ... 2016-01-26 15:13:21 6.4 STATUS COMPLETED Creating a Corresponding Section in the Report 2016-01-26 15:13:21 6.4 STATUS COMPLETED Drawing regional methylation profiles 2016-01-26 15:13:21 6.4 STATUS COMPLETED Exploratory Analysis 2016-01-26 15:13:21 6.4 INFO Initialized report index and saved to index.html 2016-01-26 15:13:21 6.4 STATUS STARTED Differential Methylation 2016-01-26 15:13:21 6.4 INFO Number of cores: 1 2016-01-26 15:13:22 6.4 STATUS STARTED Analysis 2016-01-26 15:13:22 6.4 INFO Using 0 permutation tests 2016-01-26 15:13:22 6.4 INFO Using columns: Sample_ID,Sentrix_ID,Sentrix_Position,Sample_Plate,Sample_Well,Sample_Group,Cell_Line,Passage_No,Treatment,CellType,barcode,Predicted Male Probability,Predicted Gender 2016-01-26 15:13:22 6.4 INFO Using region types: tiling,genes,promoters,cpgislands 2016-01-26 15:13:22 6.4 STATUS STARTED Retrieving comparison info 2016-01-26 15:13:22 6.4 STATUS COMPLETED Retrieving comparison info 2016-01-26 15:13:22 6.4 STATUS STARTED Computing differential methylation tables 2016-01-26 15:13:22 6.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2016-01-26 15:13:22 6.4 STATUS STARTED Computing Differential Methylation Table (Site Level) 2016-01-26 15:13:22 6.4 INFO Conducting differential analysis using limma 2016-01-26 15:14:18 6.4 STATUS COMPLETED Computing Differential Methylation Table (Site Level) 2016-01-26 15:14:19 6.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2016-01-26 15:16:48 6.4 STATUS Computed table for tiling 2016-01-26 15:17:30 6.4 STATUS Computed table for genes 2016-01-26 15:18:10 6.4 STATUS Computed table for promoters 2016-01-26 15:18:46 6.4 STATUS Computed table for cpgislands 2016-01-26 15:18:46 6.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2016-01-26 15:18:46 6.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2016-01-26 15:18:46 6.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2016-01-26 15:18:46 6.4 STATUS STARTED Computing Differential Methylation Table (Site Level) 2016-01-26 15:18:47 6.4 INFO Conducting differential analysis using limma 2016-01-26 15:19:41 6.4 STATUS COMPLETED Computing Differential Methylation Table (Site Level) 2016-01-26 15:19:41 6.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2016-01-26 15:22:26 6.4 STATUS Computed table for tiling 2016-01-26 15:23:11 6.4 STATUS Computed table for genes 2016-01-26 15:23:53 6.4 STATUS Computed table for promoters 2016-01-26 15:24:30 6.4 STATUS Computed table for cpgislands 2016-01-26 15:24:30 6.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2016-01-26 15:24:30 6.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2016-01-26 15:24:30 6.4 STATUS STARTED Comparing: CT1 vs. CT2 (based on CellType) 2016-01-26 15:24:30 6.4 STATUS STARTED Computing Differential Methylation Table (Site Level) 2016-01-26 15:24:30 6.4 INFO Conducting differential analysis using limma 2016-01-26 15:25:24 6.4 STATUS COMPLETED Computing Differential Methylation Table (Site Level) 2016-01-26 15:25:25 6.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2016-01-26 15:28:09 6.4 STATUS Computed table for tiling 2016-01-26 15:28:54 6.4 STATUS Computed table for genes 2016-01-26 15:29:36 6.4 STATUS Computed table for promoters 2016-01-26 15:30:13 6.4 STATUS Computed table for cpgislands 2016-01-26 15:30:13 6.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2016-01-26 15:30:13 6.4 STATUS COMPLETED Comparing: CT1 vs. CT2 (based on CellType) 2016-01-26 15:30:13 6.4 STATUS STARTED Comparing: female vs. male (based on Predicted Gender) 2016-01-26 15:30:13 6.4 STATUS STARTED Computing Differential Methylation Table (Site Level) 2016-01-26 15:30:14 6.4 INFO Conducting differential analysis using limma 2016-01-26 15:31:10 6.4 STATUS COMPLETED Computing Differential Methylation Table (Site Level) 2016-01-26 15:31:11 6.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2016-01-26 15:33:56 6.4 STATUS Computed table for tiling 2016-01-26 15:34:41 6.4 STATUS Computed table for genes 2016-01-26 15:35:23 6.4 STATUS Computed table for promoters 2016-01-26 15:36:00 6.4 STATUS Computed table for cpgislands 2016-01-26 15:36:00 6.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2016-01-26 15:36:00 6.4 STATUS COMPLETED Comparing: female vs. male (based on Predicted Gender) 2016-01-26 15:36:00 6.4 STATUS COMPLETED Computing differential methylation tables 2016-01-26 15:36:00 6.4 INFO Skipping enrichment analysis of differentially methylated regions 2016-01-26 15:36:00 6.4 STATUS COMPLETED Analysis 2016-01-26 15:36:00 6.4 STATUS STARTED Report Generation 2016-01-26 15:36:00 6.4 STATUS Added introductory section 2016-01-26 15:36:00 6.4 STATUS STARTED Adding Site Level Information 2016-01-26 15:36:00 6.4 STATUS STARTED Selection of rank cutoffs 2016-01-26 15:36:02 6.4 STATUS COMPLETED Selection of rank cutoffs 2016-01-26 15:36:02 6.4 STATUS STARTED Adding scatterplots 2016-01-26 15:56:32 6.4 STATUS COMPLETED Adding scatterplots 2016-01-26 15:56:32 6.4 STATUS STARTED Adding volcano plots 2016-01-26 16:05:09 6.4 STATUS COMPLETED Adding volcano plots 2016-01-26 16:05:09 6.4 STATUS STARTED Adding tables 2016-01-26 16:06:14 6.4 STATUS COMPLETED Adding tables 2016-01-26 16:06:14 6.4 STATUS COMPLETED Adding Site Level Information 2016-01-26 16:06:14 6.4 STATUS STARTED Adding Region Level Information 2016-01-26 16:06:14 6.4 STATUS STARTED Selection of rank cutoffs 2016-01-26 16:06:15 6.4 STATUS COMPLETED Selection of rank cutoffs 2016-01-26 16:06:15 6.4 STATUS STARTED Adding scatterplots 2016-01-26 16:10:24 6.4 WARNING Could not assess density colors using densCols: dim(X) must have a positive length 2016-01-26 16:12:54 6.4 WARNING Could not assess density colors using densCols: dim(X) must have a positive length 2016-01-26 16:15:55 6.4 STATUS COMPLETED Adding scatterplots 2016-01-26 16:15:55 6.4 STATUS STARTED Adding volcano plots 2016-01-26 16:20:32 6.4 STATUS COMPLETED Adding volcano plots 2016-01-26 16:20:32 6.4 STATUS STARTED Adding tables 2016-01-26 16:20:52 6.4 STATUS COMPLETED Adding tables 2016-01-26 16:20:52 6.4 STATUS COMPLETED Adding Region Level Information 2016-01-26 16:20:52 6.4 STATUS COMPLETED Report Generation 2016-01-26 16:20:52 6.4 STATUS COMPLETED Differential Methylation 2016-01-26 16:20:52 6.4 INFO Initialized report index and saved to index.html 2016-01-26 16:20:53 6.4 STATUS STARTED Saving RData 2016-01-26 16:21:12 6.4 STATUS COMPLETED Saving RData 2016-01-26 16:21:12 6.4 STATUS COMPLETED RnBeads Pipeline