I'm doing differential analysis between two groups A & B
With Fold change > 2 and FDR < 0.05 I have got more than 600 differentially expressed genes. Among them I see the following gene.
LogFC Unshrunk.logFC logCPM PValue FDR RMRP 2.802567464 2.802628518 11.43969321 1.94E-06 2.07E-05
But with Fold change > 5 and FDR < 0.05 I did not find this gene differentially expressed.
Similarly in other analysis between C & D
with Fold change > 2 and FDR < 0.05
LogFC Unshrunk.logFC logCPM PValue FDR RMRP 9.269439542 9.275584319 12.44069535 1.73E-28 1.48E-26
with Fold change > 5 and FDR < 0.05
LogFC Unshrunk.logFC logCPM PValue FDR RMRP 9.269439542 9.275584319 12.44069535 1.77E-24 8.20E-22
My question why in the analysis between A&B with Foldchange > 5 I didn't find that gene differentially expressed?
In the analysis between C & D, with Fold change > 2 and Fold Change > 5 I see the "RMRP" gene showing similar values but FDR is changing. Does FDR value change based on Fold change cutoff?