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

[Simon Anders]

Hi Delasa

On 19/06/13 19:10, Delasa Aghamirzaie wrote:
> 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?
> 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?

The p.adjust column contains p values which have been adjusted for 
multiple testing with the Benjamini-Hochberg method.

As you seem to be unfamiliar with these important concepts: A while ago, 
I tried to give an as-simple-as-possible explanation what this is about 
in this thread on SeqAnswers:
http://seqanswers.com/forums/showthread.php?t=17011

   Simon