I'm using edgeR for differential analysis between tutor and normal tissue cases.
I would like to select differential expressed genes based on log foldchange >= 2 and FDR < 0.05
Based on edgeR f1000 Research paper I used
tr <- glmTreat(fit, contrast=B.LvsP, lfc=log2(2)) which gives differential expressed genes with
FC above 2 at FDR < 0.05.
is.de <- decideTestsDGE(tr) summary(is.de) -1*Normal 1*TNBC Down 1018 NotSig 7182 Up 1535
Among those 1535 Upregulated genes I also see genes with fold change 1 and also 1.5 which are with FDR < 0.05. Don't know why it gives genes with FC 1 and 1.5 also in the results.
I need differential expressed genes with FC >= 2 & FDR < 0.05 cutoff. May I know how to get this.