Dear Sean, Thank you so much for having look at my design. Regards, Kishor On Fri, Oct 23, 2009 at 4:36 PM, Sean Davis <seandavi at="" gmail.com=""> wrote: > > > On Fri, Oct 23, 2009 at 7:00 AM, Vijay Kumar <viku781 at="" gmail.com=""> wrote: >> >> Dear Sean, >> >> I will definitely go through the documentation of topTable. But could >> you please help me with the design of the >> expreiment. >> >> I have 2 control and 2 treated. >> > > Hi, Vijay.? This is covered in the limma User Guide pretty thoroughly.? That > said, what you did below looks OK at a quick glance. > > Sean > >> >> Below is my design >> >> ? ? ? ? design <- model.matrix(~ -1+factor(c(1,1,2,2))) >> ? ? ? ? colnames(design) <- c("group1", "group2") >> ? ? ? ? contrast.matrix <- makeContrasts(group2-group1,levels=design) >> >> ? ? ? ? fit <- lmFit(data2.log, design) >> ? ? ? ? fit2 <- contrasts.fit(fit, contrast.matrix) >> ? ? ? ? fit2 <- eBayes(fit2) >> ? ? ? ? top <- topTable(fit2, coef=1, adjust="fdr", sort.by="P") >> >> Thanks, >> Vijay >> >> On Fri, Oct 23, 2009 at 4:14 PM, Sean Davis <seandavi at="" gmail.com=""> wrote: >> > >> > >> > On Fri, Oct 23, 2009 at 5:44 AM, Vijay Kumar <viku781 at="" gmail.com=""> wrote: >> >> >> >> Dear All, >> >> >> >> The topTable of LIMMA is returning adjusted P Values which are all >> >> equal to 1. What does that mean. am I doing some thing wrong. Someone >> >> please help me understand about adjusted P Values of LIMMA. >> >> >> > >> > Hi, Vijay.? You will want to read the help for the topTable() function. >> > It >> > explains how the adjustment is done. >> > >> > All the adjusted p-values equal to 1 suggests that there is no >> > differential >> > expression detected in your experiment. >> > >> > Sean >> > >> > > >