Dear Simon,
Thanks a lot for your prompt response and also the link.

Sincerely Yours,
Delasa Aghamirzaie
Genetics, Bioinformatics, and Computational Biology (GBCB) PhD Student
Virginia Tech
Blacksburg, Virginia



On Wed, Jun 19, 2013 at 1:20 PM, Simon Anders <anders@embl.de> wrote:

> 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<http://seqanswers.com/forums/showthread.php?t=17011>
>
>   Simon
>
>
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