DEG in IDEP 0.96 and IDEP 1.0

iDEP-SDSU / idep

Integrated Differential Expression and Pathway analysis

http://ge-lab.org/idep

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DEG in IDEP 0.96 and IDEP 1.0 #221

Open ysuzuki1978 opened 1 year ago

ysuzuki1978 commented 1 year ago

I ran DESeq2 at idep 0.96 and idep1.0 with FDR cutoff 0.1 and Min fold-change 2.0 settings respectively and the number of DEGs detected is significantly different. Is there something that has changed?

gun-hub commented 8 months ago

Hi, I am facing the same issue. Did you find any possible reason for the differences in the output of different versions?