Hello Steve,
Thanks for email. You have answered my question. For further quesion I will
do google search.

Thanks,
Sridhara

On Wed, Feb 23, 2011 at 4:31 PM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> Hi,
>
> On Wed, Feb 23, 2011 at 4:04 PM, Sridhara Gupta Kunjeti
> <sridhara@udel.edu> wrote:
> > Hi All,
> > I am using edgeR for the DE analysis and in the user guide I noticed to
> use
> > the following code:
> >
> > sum(p.adjust(de.common$table$p.value, method = "BH") < 0.085)
> >
> > I would appreciate, if I can have some more info on this step.
>
> You are counting the number of genes that have an adjust p-value that
> is less that 0.085
>
> > Is this step necessary do it or can we just identify the tags based on
> p-value?
>
> You are trying to combat the effect of performing a statistical test
> multiple times, see:
> http://en.wikipedia.org/wiki/Multiple_comparisons#Formalism
>
> > And also what does p.adjust mean here?
>
> It is an easy way to adjust p-values by using one of several "well
> known" p-value adjustments, see:
>
> R> ?p.adjust
>
> Google for "multiple test correction" to read up on this a bit more if
> you're still confused, or if you're not convinced that adjusting for
> multiple testing is necessary.
>
> -steve
>
>
> > Many thanks!
> > Sridhara
> >
> > --
> > Sridhara G Kunjeti
> > PhD Candidate
> > University of Delaware
> > Department of Plant and Soil Science
> > email- sridhara@udel.edu
> > Ph: 832-566-0011
> >
> >        [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> > Search the archives:
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> >
>
>
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>



-- 
Sridhara G Kunjeti
PhD Candidate
University of Delaware
Department of Plant and Soil Science
email- sridhara@udel.edu
Ph: 832-566-0011

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