Dear Robin, Please read the posting guide: http://www.bioconductor.org/help/mailing-list/posting-guide In particular, you should "Ensure that your installed packages are up-to-date" by installing the most recent release of Bioconductor. Your software is at least a couple of releases out of date. As you may have realized, your experiment has no replication. If you want to ignore the time points (treat them as replicates), then your experiment reduces to a simple two group problem, and the edgeR User Guide provides plenty of advice on how to do that. As the posting guide says, "Read the relevant R documentation". However, there are better ways to analyse your data. Are you open to a more sensible suggestion? Best wishes Gordon > Date: Thu, 1 Nov 2012 03:38:53 -0700 (PDT) > From: "R [guest]" <guest at="" bioconductor.org=""> > To: bioconductor at r-project.org, robinmjelle at gmail.com > Subject: [BioC] DE in EdgeR > > > 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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}