Changes between Version 10 and Version 11 of gene_exon_transcript_count


Ignore:
Timestamp:
Nov 12, 2013 12:50:33 PM (9 years ago)
Author:
Martijn Vermaat
Comment:

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  • gene_exon_transcript_count

    v10 v11  
    1 = Gene, exon and transcript counts =
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    4 == Counts and Spearman correlations for run 1 ==
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    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]]
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    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]]
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    15 [raw-attachment:Dstat_biobank_boxplot.pdf Boxplot of median Spearman correlations grouped by biobank] [[BR]]
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    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]]
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    24 Same mds plot but now colored according to mean GC percentage: [raw-attachment:mdsplot_filt_colored_gc.pdf mdsplot GC]
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     1This page has been moved to [wiki:FgGeneExonTranscriptCounts Gene, exon and transcript counts].