considering q- value for up/down regulated genes

Question

[ahmadvandra]

I have cuffdiff files from Illumina platform including control and treated FPKMs, log2 fold change, p-value, q-value, test stat and significance values . To choose differentially expressed genes (up/down regulated genes) respect to fold change, I would like to know whether I should only select those genes with <0.05 q- values.

Thank you in advance,

[WouterDeCoster]

Hello ahmadvandra!

It appears that your post has been cross-posted to another site: https://support.bioconductor.org/p/97173/

This is typically not recommended as it runs the risk of annoying people in both communities.

Answer 1

[venu]

I'm really not able to connect question title with the content of the question. Why a different title?

And the answer to the content of the question is - "Yes, choose genes with q.val < 0.05"

Answer 2

[theobroma22]

If you don't have any prior information suggesting a different q-value, then 0.05 is the widely accepted cut-off value. However, keep in mind this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3305783/#!po=1.00000