[BioC] edgeR: DE summary of decideTestsDGE

KJ Lim jinkeanlim at gmail.com
Mon Aug 13 12:54:09 CEST 2012

Dear edgeR and R community,

Good day.

I'm using the edgeR to analysis my RNA-Seq data which contained 2
genotype (HS,LS) and different time points (0H, 3H, 24H, 96H). The
differential analysis was carried out based on the guide of the latest
edgeR user's guide (Chapter 3, section 3.3).

May I ask it that common to obtain the summary of differentially
express (DE) genes like below? The number of DE genes seemed very
little in my case, HS vs LS at 24H

  > summary(dt.hvsl24h <- decideTestsDGE(lrt.hvsl24h,
adjust.method="BH", p.value=0.05))
  -1     3
  0  46997
  1      4

The summary of DE genes was none when I carried out the decideTestDGE
for the HS vs LS at 96H. May I ask is that common or I have done
something wrong in between?

Thank you very much for your time and advice.

Have a nice day.

Best regards,
KJ Lim

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