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3.6 years 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
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?
i have done this in galaxy NGS-RNAseq of two samples.
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.
cool. So, do we take p-value or adj p-value??
Adjusted p-value since only this controls the FDR.