| 1 | | = Gene, exon and transcript counts = |
| 2 | | |
| 3 | | |
| 4 | | == Counts and Spearman correlations for run 1 == |
| 5 | | |
| 6 | | Date: 06-november-2013[[BR]] |
| 7 | | Analysis by: Peter-Bram 't Hoen[[BR]] |
| 8 | | |
| 9 | | The combined gene counts for the 2330 samples from run 1 are available on the VM: /virdir/Backup/run_1_gene_counts/combined_gene_count_run_1.txt and were generated using this script: [raw-attachment:merge_count_script.r R script for merging gene count tables][[BR]] |
| 10 | | Subsequently, pairwise Spearman correlations were calculated: /virdir/Backup/run_1_gene_counts/Spearman_correlations_complete_gene_data_run_1.txt[[BR]] |
| 11 | | From these the median Spearman correlation for each sample to each other sample was calculated. This is also called the D-statistic. The D-statistics (ranked from low to high) can be found in this file [raw-attachment:Median_pairwise_spearman_correlations_complete_gene_data_run_1.txt Median Spearman correlations][[BR]] |
| 12 | | |
| 13 | | [raw-attachment:Median_pairwise_spearman_correlations_by_flowcell_complete_gene_data_run_1.pdf Boxplot of median Spearman correlations grouped by flowcell] (Martijn Vermaat)[[BR]] |
| 14 | | |
| 15 | | [raw-attachment:Dstat_biobank_boxplot.pdf Boxplot of median Spearman correlations grouped by biobank] [[BR]] |
| 16 | | |
| 17 | | After removing the two samples with very low Spearman correlations to all other samples, the distance matrix was calculated (1 - correlation matrix), and a two-dimensional MDS plot was created using the R function cmdscale. [raw-attachment:mdsplot_filt_colored_biobank.pdf This is the resulting mdsplot]. The plot was colored according to the following color scheme: [[BR]] |
| 18 | | "LL" - gold[[BR]] |
| 19 | | "RS" - blue[[BR]] |
| 20 | | "CODAM" - orange[[BR]] |
| 21 | | "LLS" - pink[[BR]] |
| 22 | | "Amsterdam" - darkred[[BR]] |
| 23 | | |
| 24 | | Same mds plot but now colored according to mean GC percentage: [raw-attachment:mdsplot_filt_colored_gc.pdf mdsplot GC] |
| 25 | | |
| 26 | | |
| | 1 | This page has been moved to [wiki:FgGeneExonTranscriptCounts Gene, exon and transcript counts]. |
