Perform DE analysis
Last updated
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Last updated
Was this helpful?
We will now perform differential gene expression analysis using R.
Download the above R script, save in the LSLNGS2015 folder, unzip and run
cd ~/LSLNGS2015
Rscript --vanilla run_edgeR.R
Output shown in the terminal
Loading required package: limma
Loading required package: methods
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The R script output and save the results of the analysis into 2 files: DE_analysis.gene.txt
and DE_analysis.transcript.txt
.
head DE_analysis.gene.txt
chr left right gid score strand name source biotype logFC logCPM F PValue FDR
1 14403 29570 ENSG00000227232 . - WASH7P havana unprocessed_pseudogene 2.89008492452335 2.97744129628027 103.370995316555 8.24483666908638e-09 3.265037563718e-08
1 89294 133723 ENSG00000238009 . - RP11-34P13.7 ensembl_havana lincRNA 11.5139234165179 1.60559878078354 167.167165147925 2.10113367749614e-10 1.2064846331368e-09
1 135140 135895 ENSG00000268903 . - RP11-34P13.15 havana processed_pseudogene 5.06459149590687 0.0881194042027241 42.478504740963 6.16479106039061e-06 1.38838943956985e-05
1 184922 200322 ENSG00000279457 . - FO538757.1 ensembl protein_coding 1.69721957446631 1.80636207182208 24.1093251919636 0.000103795172528207 0.000194091404654342
1 257863 297502 ENSG00000228463 . - AP006222.2 havana lincRNA 13.0394746095367 3.07489541107415 477.124570057853 3.59556529227458e-14 4.97461947310632e-13
1 629639 630683 ENSG00000225630 . + MTND2P28 havana unprocessed_pseudogene 3.13735915488644 4.44862764583624 199.762650496711 3.1768017645391e-10 1.76596074752208e-09
1 631073 632616 ENSG00000237973 . + MTCO1P12 havana unprocessed_pseudogene 0.443696840509747 4.12363294925077 6.13472027306747 0.02307860917183 0.0308376479322919
1 633695 634376 ENSG00000248527 . + MTATP6P1 havana unprocessed_pseudogene 1.34550546639341 5.77825431060693 3.37645905964982 0.191889704720111 0.224260991075299
1 725884 778626 ENSG00000228327 . - RP11-206L10.2 havana transcribed_unprocessed_pseudogene 1.88938948596173 2.34383806326781 33.6517600212232 1.78166537736188e-05 3.74464140783175e-05
head DE_analysis.transcript.txt
chr left right tid score strand name source biotype logFC logCPM F PValue FDR
1 34553 36081 ENST00000417324 . - FAM138A havana lincRNA 14.7287711778192 4.74754988064348 855.407406314551 9.10858850487461e-05 0.00433065266019644
1 110952 129173 ENST00000471248 . - RP11-34P13.7 ensembl_havana lincRNA -11.6703832090145 1.69559510020159 212.015384690327 0.000721411986621592 0.0087655978717093
1 135140 135895 ENST00000494149 . - RP11-34P13.15 havana processed_pseudogene 0.335112637932721 0.296069849428322 0.0990772814490298 0.768783599380141 0.826519388419821
1 165888 168767 ENST00000491962 . - RP11-34P13.13 havana processed_transcript 0.653389858107978 2.37876611393755 2.69735804942855 0.176126586222385 0.266941473371366
1 257863 264733 ENST00000442116 . - AP006222.2 havana lincRNA 2.10853347357073 1.82097762397731 30.5633854683598 0.00528769030910118 0.0209971307641988
1 258567 259024 ENST00000450734 . - RPL23AP21 havana processed_pseudogene 1.85301838291288 3.06998220640272 13.5659404366886 0.0212839694345138 0.0554117574914843
1 266360 297502 ENST00000424587 . - AP006222.2 havana lincRNA -10.8844390575141 0.915559268435426 124.294800531017 0.00158219973633488 0.0119137545202454
1 347981 348366 ENST00000458203 . - RPL23AP24 havana processed_pseudogene 1.76650999454457 1.51923976505446 7.9898205742989 0.0477136055714843 0.0994641817520193
1 357382 359681 ENST00000441866 . - RP5-857K21.15 havana lincRNA 0.260927151869554 0.438550143910703 0.120976329938423 0.745572526693337 0.807497648960747
MDS plot shows clear separation of the GM12878 versus K562 samples.
The plotMD()
from limma generate mean difference plot displaying the log fold changes and average expression values for each gene (or M versus A plot or MA plot).
The differentially expressed genes (adjusted P = 0.05) are highlighted in red.