Dear all, I am just a little bit confused about p.value, adj.p.value and F.p.value. Could somebody tell me what are the proper cases to use them? I am supposed to detect the differenct expressed genes with the p-value less than 0.05, therefore, my code is like follows: fit<-eBayes(fit) selected<-p.value<0.05 But in Limma user guide, the code is like this: selected<-p.adjust(fit$F.p.value, method="BH") <0.05 here the F.p.value is used. And also if i choose the top10 different expressed genes like this: topTable(fit, adjust="BH") there is a adj.p.value. So I really want to know when to use which. Expecting your reply. Regards, Yanju

Hi, Yan Jun: You can check some infomation on the multiple testing correction, BH represents Benjamini & Hochberg (1995) method, which defines a sequential p-value, a procedure that controls expected FDR. you probably need to do some literature reading to understand why multiple testing procedure is neccessary. hth, weiwei On 11/27/06, yanju <yanju at="" liacs.nl=""> wrote: > Dear all, > > I am just a little bit confused about p.value, adj.p.value and > F.p.value. Could somebody tell me what are the proper cases to use them? > I am supposed to detect the differenct expressed genes with the p-value > less than 0.05, therefore, my code is like follows: > fit<-eBayes(fit) > selected<-p.value<0.05 > > But in Limma user guide, the code is like this: > selected<-p.adjust(fit$F.p.value, method="BH") <0.05 > here the F.p.value is used. > > And also if i choose the top10 different expressed genes like this: > topTable(fit, adjust="BH") > there is a adj.p.value. > > So I really want to know when to use which. Expecting your reply. > > Regards, > Yanju > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III