thanks On Fri, Sep 30, 2011 at 5:25 PM, Francois Pepin < francois.pe...@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.pe...@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. > > > > > > > > > [[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 and provide commented, minimal, self-contained, reproducible code.
