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]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > -- > 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 [[alternative HTML version deleted]]