Question: considering q- value for up/down regulated genes
0
gravatar for ahmadvandra
22 months 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 • 918 views
ADD COMMENTlink modified 22 months ago by theobroma221.1k • written 22 months 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 22 months ago by WouterDeCoster38k
2
gravatar for venu
22 months ago by
venu6.1k
Germany
venu6.1k 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 22 months ago • written 22 months ago by venu6.1k
1
gravatar for theobroma22
22 months 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 22 months ago by theobroma221.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 777 users visited in the last hour