Dear R helpers, I'm an biologist and very new to R. I've read 'sva' and 'limma' packages. Would you please enlighten me about the design of model.matrix in 'sva' vignette? In page 4 of the vignette, what will the whole script look like if I design the full model matrix (Let's say ???mod1???) as following mod1 = model.matrix(~0 + as.factor(cancer), data=pheno) I try to follow the all steps using ???mod1???, then end up with confusion due to my limited knowledge. Please guide me. With respects, Kaj -- output of sessionInfo(): R version 3.0.2 (2013-09-25) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] splines parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] limma_3.16.8 pamr_1.54.1 survival_2.37-4 cluster_1.14.4 [5] bladderbatch_1.0.5 Biobase_2.20.1 BiocGenerics_0.6.0 sva_3.6.0 [9] mgcv_1.7-27 nlme_3.1-113 corpcor_1.6.6 loaded via a namespace (and not attached): [1] grid_3.0.2 lattice_0.20-24 Matrix_1.1-0 tools_3.0.2 -- Sent via the guest posting facility at bioconductor.org.