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considering q- value for up/down regulated genes

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,

rna-seq
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updated by theobroma22 theobroma22 • written by ahmadvandra • ahmadvandra

2 answers

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"

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written by venu venu

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

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written by theobroma22 theobroma22

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