Question: I do not find DEG's with EdgeR that I do find with other tools
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gravatar for zoe
15 months ago by
zoe0
zoe0 wrote:

I am comparing different RNA-seq pipelines to find differentially expressed genes. With those pipelines I am comparing three groups: control, samples of mice 6 hours after infection and 24 hours after infection. With most of the R analysis tools I find differentially expressed genes between all groups, but when I use EdgeR I only find DEG's between 6 hour and control and sometimes also between 24 hour and control. What could be the reason I never find any DEG's when I compare 24 hr with 6 hr using Edger, even if I find a lot of genes when I use NOISeq or Ballgown. Thanks a lot!

rna-seq • 458 views
ADD COMMENTlink written 15 months ago by zoe0

How many replicates you have per condition ?

ADD REPLYlink written 15 months ago by geek_y9.8k

for the control and the 6 hour samples I have 3 replicates, for the 24 hour samples I have 2

ADD REPLYlink written 15 months ago by zoe0
1

If you have 2-3 replicates, its hard to judge the reproducibility. How many genes were DE between 6h and 24h with other tools ?

P.S What do you mean by other tools ?

ADD REPLYlink written 15 months ago by geek_y9.8k

NOIseq and Ballgown are mentioned in orig post.

ADD REPLYlink written 15 months ago by genomax71k

With ballgown and noiseq I get between 250 and 400 DEG (depending on the upstream tools)

ADD REPLYlink written 15 months ago by zoe0

Are you expecting many differentially expressed genes? Sometimes it is a good thing to only get a few...

EdgeR normalises via TMM, whilst NOIseq and Ballgown may be normalising via upper-quartile, RPKM, or something else. You can tell us which normalisation method you used in both NOIseq and Ballgown.

ADD REPLYlink written 15 months ago by Kevin Blighe48k
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