Hello, all I am confused by the adjPval from maanova and qvalue. I am not sure after I use the matest , which one I should use if I want to take a look at the FDR. Should I compute the q-values of these adjusted P-values or just use the original p-values to compute the corresponding q-values. Or I have some misunderstanding about q-values and adjusted pvalues. Thanks Sabrina

sabrina.shao wrote: > Hello, all > I am confused by the adjPval from maanova and qvalue. I am not sure > after I use the matest , which one I should use if I want to take a look > at the FDR. Should I compute the q-values of these adjusted P-values or > just use the original p-values to compute the corresponding q-values. Or > I have some misunderstanding about q-values and adjusted pvalues. Thanks I think you are confused. The matest() function doesn't compute adjusted p-values. It computes permuted p-values which is a different thing. Anyway, the example for adjPval() pretty much outlines the steps you should be taking: data(paigen) paigen <- createData(paigen.raw, n.rep=2) model.noint.fix <- makeModel(data=paigen, formula=~Array+Dye+Spot+Strain+Diet) # F-test strain effect ## Not run: test.strain.fix <- matest(paigen, model.noint.fix, term="Strain", n.perm=100, shuffle.method="resid", test.method=rep(1,4)) # make FDR adjusted P values test.strain.fix <- adjPval(test.strain.fix) ## End(Not run) # there will be new fields in test.strain.fix after this Best, Jim > > Sabrina > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.