thanks

On Fri, Sep 30, 2011 at 5:25 PM, Francois Pepin <
francois.pepin@sequentainc.com> wrote:

> Hi Jiang,
>
> where did you get that definition of the Benjamini-Hochberg correction?
> That is simply not how it works. You can take a look at the original paper,
> it is available online (
> http://www.math.tau.ac.il/~ybenja/MyPapers/benjamini_hochberg1995.pdf).
> You can also look at the p.adjust function to see how it is implemented in
> R.
>
> Also, please keep the replies on the list. They're archived so that other
> people can refer to it later it also gives other people the opportunity to
> reply if they have more to add.
>
> Francois
>
> On Sep 30, 2011, at 15:07 , chunjiang he wrote:
>
> > Hi Francois,
> >
> > Thansk for your reply. I did BH correction manually. Just use corrected
> pvalue=pvalue*(n/n-1). And I got the result like this: The pvalue in manual
> and by R package are different.
> >
> > title r       raw     R package       manual
> > hsa-miR-205--GATA3    0.797883        1.08E-13        1.08E-12
>  1.08E-12
> > hsa-miR-205--ITGB4    0.750218        1.85E-11        8.20E-11
>  9.25E-11
> > hsa-miR-187--PGF      0.797604        3.24E-11        8.20E-11
>  1.08E-10
> > hsa-miR-205--SERPINB5 0.744125        3.28E-11        8.20E-11
>  8.20E-11
> > hsa-miR-205--PBX1     0.734487        7.89E-11        1.58E-10
>  1.58E-10
> > hsa-miR-205--MCC      0.724999        1.80E-10        3.00E-10
>  3.00E-10
> > hsa-miR-205--WNT5B    0.717705        3.33E-10        3.78E-10
>  4.76E-10
> > hsa-miR-200c--PKN2    0.721747        3.46E-10        3.78E-10
>  4.33E-10
> > hsa-miR-200c--PCYOX1  0.721698        3.48E-10        3.78E-10
>  3.87E-10
> > hsa-miR-200c--WDR68   0.72068 3.78E-10        3.78E-10        3.78E-10
> >
> > So I am confused about that.
> >
> > Best,
> > Jiang
> > On Fri, Sep 30, 2011 at 4:53 PM, Francois Pepin <
> francois.pepin@sequentainc.com> wrote:
> > Hi Jiang,
> >
> > you'll have to give us some more information than this: a reproducible
> example and why you expect things to be different.
> >
> > This method has been tested extensively so we'd need something more
> specific if we are to help you.
> >
> > Francois
> >
> > On Sep 30, 2011, at 14:40 , chunjiang he wrote:
> >
> > > Hi,
> > >
> > > There is a question that I am confused.
> > > I have a set of data like this:
> > >
> > > hsa-miR-205--GATA3    0.797882767 1.08E-13
> > > hsa-miR-205--ITGB4     0.750217593 1.85E-11
> > > hsa-miR-187--PGF        0.797604155 3.24E-11
> > > hsa-miR-205--SERPINB5 0.744124886 3.28E-11
> > > hsa-miR-205--PBX1 0.734487224 7.89E-11
> > > hsa-miR-205--MCC 0.72499934 1.80E-10
> > > hsa-miR-205--WNT5B 0.717705259 3.33E-10
> > > hsa-miR-200c--PKN2 0.721746815 3.46E-10
> > > hsa-miR-200c--PCYOX1 0.721698034 3.48E-10
> > > hsa-miR-200c--WDR68 0.72068017 3.78E-10
> > >
> > > And I want to do the Benjamini & Hochberg correction.
> > >
> > > So I run :
> > >
> > > rm(list=ls())
> > > a<-read.csv("1-correlation.txt",sep="\t",header=F,quote="")
> > > c<-p.adjust(a$V3,"BH")
> > > a[,4]<-c
> > > write.table(a,"zz.txt",sep="\t")
> > >
> > > And I got the result:
> > >
> > > hsa-miR-205--GATA3 0.797882767 1.08E-13 1.08E-12
> > > hsa-miR-205--ITGB4 0.750217593 1.85E-11 8.20E-11
> > > hsa-miR-187--PGF 0.797604155 3.24E-11 8.20E-11
> > > hsa-miR-205--SERPINB5 0.744124886 3.28E-11 8.20E-11
> > > hsa-miR-205--PBX1 0.734487224 7.89E-11 1.58E-10
> > > hsa-miR-205--MCC 0.72499934 1.80E-10 3.00E-10
> > > hsa-miR-205--WNT5B 0.717705259 3.33E-10 3.78E-10
> > > hsa-miR-200c--PKN2 0.721746815 3.46E-10 3.78E-10
> > > hsa-miR-200c--PCYOX1 0.721698034 3.48E-10 3.78E-10
> > > hsa-miR-200c--WDR68 0.72068017 3.78E-10 3.78E-10
> > >
> > > When I check it, I found some adjust pvalue are not same to result that
> I
> > > did manually.
> > >
> > > Can anyone help for this. Thanks,
> > >
> > > Jiang
> > >
> > >       [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
> > > R-help@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> > > and provide commented, minimal, self-contained, reproducible code.
> >
> >
> >
>
>
>

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