limma User's Guide, Section 8.3 "Paired samples". Adding covariates is no problem. Best wishes Gordon > Date: Thu, 31 Jul 2008 11:33:12 -0400 > From: "Chunyan Liu" <chunyan.liu at="" cchmc.org=""> > Subject: [BioC] Can limma be used to the matched data? > To: <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <4891A2F80200000600532ADD at n6mcgw16.cchmc.org> > Content-Type: text/plain; charset=US-ASCII > > Hi, > > Could someone tell me if limma can be used for matched data? If not, any > suggestions? The cases and controls were age, gender and race matched. I > could have just used paired t test and adjust for multiple comparisons. > But I would like the possibility to adjust for other covariates. Does > anyone have similar situation? > > Thanks. > > Chunyan Liu > Biostatistician I > Center for Epidemiology and Biostatistics > Cincinnati Children's Hospital Medical Center > 513-636-9763