Roth, Richard wrote: > Hi, I have a data matrix of gene expression data from two groups that > I would like to compare using the t-test. The data has been > processed using RMA and transformed using log2. I would like to > compare the two groups for each gene (N=10,000 genes) and have a > result that lists the p-value for each test. Can anyone help me with > the t.test setup for this analysis?
Take a look at the limma package in BioConductor. You will be able to do what you want much faster than using e.g., t.test(). There is an extensive user's guide that should help you figure out what to do. HTH, Jim > > Thanks, Rich > > Rich Roth, PhD Senior Scientist Molecular Medicine Neurocrine > Biosciences 858-617-7204 > > > > > ------------------------------------------------------------------------ > > > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the > posting guide! http://www.R-project.org/posting-guide.html -- 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 ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
