Hi James, thank you very much for taking a look at my question. Your answer will help a lot. Best regards Jorge On Tue, Aug 28, 2012 at 4:44 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Jorge, > > > On 8/28/2012 10:34 AM, Jorge Miró wrote: > >> Hi, >> >> I am trying to understand how to make the design matrix and the contrat >> matrix for my analysis of gene expressions but I really can't figure it >> out. >> What I have is 9 arrays where three of them correspond to untreated >> individuals (groupA), another three correpond to a low level of treatment >> (groupB) and the last three to a higher level of treatment (groupC). What >> I >> want to do is to compare the treatments and check what genes have been >> affected in some kind of loop design, i.e groupA compared with >> groupB, groupA compared with groupC and groupB compared with groupC. >> I have read in the limma user guide and think a design matrix like the one >> below could do what I want but I'm really not sure if I'm doing something >> wrong: >> > > Looks good to me. > > Best, > > Jim > > > >> #COntruct design matrix >> >>> design<- model.matrix(~ 0+factor(c(1,1,1,2,2,2,3,3,3))**) >>> colnames(design)<- c('GroupA', 'GroupB', 'GroupC') >>> >> #Contruct contrast matrix >> >>> contrast.matrix<- makeContrasts(GroupB-GroupA, GroupC-GroupA, >>> >> GroupC-GroupB, levels=design) >> >> #Print design matrix >> >>> design >>> >> GroupA GroupB GroupC >> 1 1 0 0 >> 2 1 0 0 >> 3 1 0 0 >> 4 0 1 0 >> 5 0 1 0 >> 6 0 1 0 >> 7 0 0 1 >> 8 0 0 1 >> 9 0 0 1 >> attr(,"assign") >> [1] 1 1 1 >> attr(,"contrasts") >> attr(,"contrasts")$`factor(c(**1, 1, 1, 2, 2, 2, 3, 3, 3))` >> [1] "contr.treatment" >> >> #Print contrast matrix >> >>> contrast.matrix >>> >> Contrasts >> Levels GroupB - GroupA GroupC - GroupA GroupC - GroupB >> GroupA -1 -1 0 >> GroupB 1 0 -1 >> GroupC 0 1 1 >> >> >> #Session info >> >>> sessionInfo() >>> >> R version 2.15.0 (2012-03-30) >> Platform: i386-pc-mingw32/i386 (32-bit) >> >> locale: >> [1] LC_COLLATE=Swedish_Sweden.1252 LC_CTYPE=Swedish_Sweden.1252 >> LC_MONETARY=Swedish_Sweden.**1252 LC_NUMERIC=C >> LC_TIME=Swedish_Sweden.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] limma_3.12.1 Biobase_2.16.0 BiocGenerics_0.2.0 >> >> loaded via a namespace (and not attached): >> [1] affylmGUI_1.30.0 IRanges_1.14.4 oneChannelGUI_1.22.10 >> stats4_2.15.0 tcltk_2.15.0 >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > [[alternative HTML version deleted]]