Question: considering q- value for up/down regulated genes
0
gravatar for ahmadvandra
2.3 years ago by
ahmadvandra0 wrote:

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 • 1.1k views
ADD COMMENTlink modified 2.3 years ago by theobroma221.1k • written 2.3 years ago by ahmadvandra0

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.

ADD REPLYlink written 2.3 years ago by WouterDeCoster41k
2
gravatar for venu
2.3 years ago by
venu6.3k
Germany
venu6.3k wrote:

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"

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by venu6.3k
1
gravatar for theobroma22
2.3 years ago by
theobroma221.1k
theobroma221.1k wrote:

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

ADD COMMENTlink written 2.3 years ago by theobroma221.1k
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