hi all, I have datasets derived from RNAseq experiments (each experiment is the effect of one drug on a cancer) ,I did differential expression.for identifying differential expression,I had 3 statistical test: t-test,DGE and Beggerly test.in next step I should filter some genes by high fold change and low FDR p-value (I used Fold change ≥ 1.5 FDR P-VALUE ≤ .05 )

But the problem starts,for one experiment t-test gives the appropriate number of genes, in another one, Beggerly test gives a suitable number of genes and t-test doesn't answer ,also in some experiments there are lots of genes even with these filters or in each 3 test I have a lot of genes.

what should I do?should I use different type of test for each experiment and On what basis should I choose statistical test؟

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dear Farbod,thank you for a replay.because of my supervisor!I should use CLC genomics for my thesis

Sounds like a good time to start ignoring your advisor.