I have a doubt in how to find out differential expressed genes in deseq2
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13 months ago

Hello. I am new to NGS Rna-Seq. Could anyone help me out with how can i know the differential expressed genes from Deseq2. I got output as like below. I appreciate for ur answer and time.

GeneID  Base mean   log2(FC)    StdErr  Wald-Stats  P-value P-adj
79986   1098.47707308976    -1.11150159213833   0.12558382171767    -8.85067500682649   8.69915355094096e-19    1.85030996028514e-14
23461   8573.47869431982    -0.734252367507201  0.0922478981618111  -7.95955660929268   1.72656864565224e-15    1.83620575465116e-11
9585    706.214830073438    -1.04806578975518   0.134843384669255   -7.77246723912996   7.6971916551589e-15 5.45730888350766e-11
6271    408.296492902145    1.30858235403647    0.170035883254148   7.69591882015029    1.40480983755747e-14    7.47007631121182e-11
284702  1890.39708476505    -0.841992239572733  0.115266181684671   -7.3047638714722    2.77754079799892e-13    9.84638212890617e-10
9781    6469.93787966689    -0.738045872804328  0.100969376968143   -7.30960113814697   2.67936520072918e-13    9.84638212890617e-10
55023   9451.97990560052    -0.679538111098682  0.0944304548490097  -7.1961753460283    6.19249847417473e-13    1.88163489350995e-09
101926935   598.759881903342    -1.02766929266615   0.144103812860554   -7.13145108561845   9.93162490955181e-13    2.64057077282709e-09

next-gen rna-seq sequence RNA-Seq • 394 views
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I recommend to exactly follow the manual which contains all necessary code: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html

This above does not look like the native output of DESeq2, what is it?

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i have done this in galaxy NGS-RNAseq of two samples.

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I see. Please ask Galaxy-specific questions over at the Galaxy community: https://help.galaxyproject.org/ if you want to further manipulate this file in Galaxy.

In general (even though I do not know how this table was created) you can simply filter by adjusted p-value being smaller than e.g. 0.05 which is a common threshold. All genes below this threshold you can then consider to be DE.

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cool. So, do we take p-value or adj p-value??

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Adjusted p-value since only this controls the FDR.