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Question: How to calculate q value in rna-seq data?
1
gravatar for --panda--
2.8 years ago by
--panda-- • 30
Evanston
--panda-- • 30 wrote:

In fact, it is quite a statistical question rather than biological question. After we compare the expression data and get the p value for different genes(iso forms, tss, or any other groups of interest), people sometimes need to control FDR(false discovery rate). Here is the method used in cufflinks to achieve this goal (a wiki page, not from the cufflinks paper): Wiki page

I understand the steps used here, but I don't know how can the software come up with a q value based on this procedure.
rna-seq • 1.7k views
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modified 2.8 years ago by Nicolas Rosewick ♦ 7.6k • written 2.8 years ago by --panda-- • 30
2
gravatar for Nicolas Rosewick
2.8 years ago by
Nicolas Rosewick ♦ 7.6k
Belgium, Brussels
Nicolas Rosewick ♦ 7.6k wrote:

In R if p is a vector of pvalues then use : q <- p.adjust(p,method="fdr") or use the qvalue package :https://www.bioconductor.org/packages/release/bioc/html/qvalue.html
ADD COMMENT • link modified 2.8 years ago • written 2.8 years ago by Nicolas Rosewick ♦ 7.6k

Um, is there any description about the math under this transformation?

ADD REPLY • link written 2.8 years ago by --panda-- • 30

In the R vignette you have all the references to the original papers : https://stat.ethz.ch/R-manual/R-devel/library/stats/html/p.adjust.html

And for the q-value package : J. D. Storey. False discovery rates. In Miodrag Lovric, editor, International Encyclopedia of Statistical Science. Springer, 2011. : http://genomine.org/papers/Storey_FDR_2011.pdf

ADD REPLY • link modified 2.8 years ago • written 2.8 years ago by Nicolas Rosewick ♦ 7.6k

Thanks! That's really useful.

ADD REPLY • link written 2.8 years ago by --panda-- • 30
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