Search
Question: adjPval and qvalue
0
gravatar for sabrina.shao
11.7 years ago by
sabrina.shao220
sabrina.shao220 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 Sabrina
ADD COMMENTlink modified 11.7 years ago by James W. MacDonald45k • written 11.7 years ago by sabrina.shao220
1
gravatar for James W. MacDonald
11.7 years ago by
United States
James W. MacDonald45k wrote:
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.
ADD COMMENTlink written 11.7 years ago by James W. MacDonald45k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 206 users visited in the last hour