Hello BioC forum, I am making a design matrix for gene expression data analysis with the adjustment of Sex variable. The R code I am using is below. I want to make sure if I am doing correctly. Thanks for your review and feedback. > library(limma) > Sample<-factor(pd$Sample_Group, levels=c("Control","Case")) ### treatment > Sex<-factor(pd$Sex, levels=c("M","F")) ### Sex > design<-model.matrix(~Sample+Sex) > design (Intercept) SampleCase SexF 1 1 0 0 2 1 0 0 3 1 0 0 4 1 0 1 5 1 0 1 6 1 0 1 7 1 1 1 8 1 0 0 9 1 0 1 10 1 1 0 11 1 1 1 12 1 0 1 13 1 0 1 14 1 1 0 15 1 0 0 16 1 1 1 17 1 0 0 18 1 0 0 19 1 1 0 20 1 0 0 21 1 0 1 22 1 1 1 23 1 0 1 24 1 0 0 25 1 1 0 26 1 0 1 27 1 0 1 28 1 0 1 29 1 0 0 30 1 0 0 31 1 1 1 32 1 0 1 33 1 0 1 34 1 1 0 35 1 0 0 attr(,"assign") [1] 0 1 2 attr(,"contrasts") attr(,"contrasts")$Sample [1] "contr.treatment" attr(,"contrasts")$Sex [1] "contr.treatment" > colnames(design) [1] "(Intercept)" "SampleCase" "SexF" > Lmfit<-lmFit(autosome.Mvalues.noSNPs, design) ## using M values > fit<-eBayes(Lmfit) > top.50<-topTable(fit,coef=2,adjust.method="fdr",number=50,sort.by="B") > top.50 -- output of sessionInfo(): > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] FlowSorted.Blood.450k_1.2.0 quadprog_1.5-5 [3] DMRcate_1.0.1 DMRcatedata_1.0.0 [5] limma_3.20.8 ks_1.9.2 [7] rgl_0.93.1098 mvtnorm_1.0-0 [9] misc3d_0.8-4 KernSmooth_2.23-12 [11] minfiData_0.6.0 IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 [13] IlluminaHumanMethylation450kmanifest_0.4.0 minfi_1.10.2 [15] bumphunter_1.4.2 locfit_1.5-9.1 [17] iterators_1.0.7 foreach_1.4.2 [19] Biostrings_2.32.1 XVector_0.4.0 [21] GenomicRanges_1.16.4 GenomeInfoDb_1.0.2 [23] IRanges_1.22.10 lattice_0.20-29 [25] Biobase_2.24.0 BiocGenerics_0.10.0 loaded via a namespace (and not attached): [1] annotate_1.42.1 AnnotationDbi_1.26.0 base64_1.1 beanplot_1.1 codetools_0.2-8 [6] DBI_0.2-7 digest_0.6.4 doRNG_1.6 genefilter_1.46.1 grid_3.1.0 [11] illuminaio_0.6.0 MASS_7.3-33 matrixStats_0.10.0 mclust_4.3 multtest_2.20.0 [16] nlme_3.1-117 nor1mix_1.1-4 pkgmaker_0.22 plyr_1.8.1 preprocessCore_1.26.1 [21] R.methodsS3_1.6.1 RColorBrewer_1.0-5 Rcpp_0.11.2 registry_0.2 reshape_0.8.5 [26] rngtools_1.2.4 RSQLite_0.11.4 siggenes_1.38.0 splines_3.1.0 stats4_3.1.0 [31] stringr_0.6.2 survival_2.37-7 tools_3.1.0 XML_3.98-1.1 xtable_1.7-3 [36] zlibbioc_1.10.0 -- Sent via the guest posting facility at bioconductor.org. _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor