[BioC] p-value vs adjusted p-value in DEXSeq

[Richard Friedman]

On Jun 19, 2013, at 1:10 PM, Delasa Aghamirzaie wrote:

> Hi,
> I have used DEXSeq for differential exon usage testing. I believe  what
> DEXSeq uses as threshold for finding significant differentially expressed
> exons is p-adjust < 0.1 and it reports both p-value and p-adjust in its
> results.
> My question is that what is the difference between p-adjust and p-value?

Dear Delasa,

	I am not sure which option p-adjust you used but if it is the Benjamini-Hochberg
false discovery rate it estimates how many genes which were accepted as differentially
expressed based on the cutoff are in fact not differentially expressed. 
Fdr is more stringent than p-value but does not have to have as low a value.
Say you usea p-value cutoff <0.05. As long as this value is not
exceeded it is resonable to take p-adjust (fdr) at 0.1 or even as high as 0.5 
as long as you know that in the latter case have the genes you try to validate
by pcr are expected not to be differentially expressed. I think that p-adjust<0.05-0.25
are good cutoffs.

With hopes that the above helps,
Rich
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)/
Columbia Initiative in Systems Biology
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

In Memroriam, John Holbrook Vance







> when I use p-adjjust < 0.1 as threshold, I get a few number of genes, while
> in the case of p-value < 0.05, I get ,much more genes. I was wondering
> which threshold is more accurate?
> 
> Sincerely Yours,
> Delasa Aghamirzaie
> Genetics, Bioinformatics, and Computational Biology (GBCB) PhD Student
> Virginia Tech
> Blacksburg, Virginia
> 
> 	[[alternative HTML version deleted]]
> 
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