I am testing DE between two groups that each contain 10 time points. I am creating my design matrix like this: Condition <- factor(c("KO","KO","KO","KO","KO","KO","KO","KO","KO","WT ","WT","WT","WT","WT","WT","WT","WT","WT")) Condition <- relevel(Condition, ref="WT") Time <- factor(c("0H","3H","6H","9H","12H","18H","21H","24H","27H","0H ","3H","6H","9H","12H","18H","21H","24H","27H")) design <- model.matrix(~Time+Time:Condition) How do I proceed if i want to compare the whole group (WT) against the other group (KO) considering the time points as replicates. -- output of sessionInfo(): R version 2.14.1 (2011-12-22) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=nb_NO.UTF-8 LC_NUMERIC=C LC_TIME=nb_NO.UTF-8 [4] LC_COLLATE=nb_NO.UTF-8 LC_MONETARY=nb_NO.UTF-8 LC_MESSAGES=nb_NO.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=nb_NO.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.2.1 DESeq_1.6.1 locfit_1.5-8 org.Mm.eg.db_2.6.4 [5] RSQLite_0.11.2 DBI_0.2-5 AnnotationDbi_1.16.19 Biobase_2.14.0 [9] edgeR_2.4.6 limma_3.10.3 loaded via a namespace (and not attached): [1] annotate_1.32.3 genefilter_1.36.0 geneplotter_1.32.1 grid_2.14.1 [5] IRanges_1.12.6 lattice_0.20-0 RColorBrewer_1.0-5 survival_2.36-10 [9] tools_2.14.1 xtable_1.7-0 -- Sent via the guest posting facility at bioconductor.org.