considering q- value for up/down regulated genes
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3.9 years ago

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 • 1.6k views
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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.

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3.9 years ago
venu 6.8k

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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3.9 years ago
theobroma22 ★ 1.1k

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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