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!
Question: I do not find DEG's with EdgeR that I do find with other tools
15 months ago by
zoe • 0
zoe • 0 wrote:
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