Dear Anders, Thanks for the bug report and the reproducible example. The problem is fixed in edgeR 1.5.4. Note that you could also specify the contrast by pair=c(1,3) instead of c("A","C"). Best wishes Gordon > library(edgeR) > library( edgeR ) > counts <- matrix( rnbinom( 600, 5, .1 ), ncol=6 ) > conds <- c( "A", "A", "B", "B", "C", "C" ) > dgl <- DGEList( counts=counts, group=conds ) Warning message: In DGEList(counts = counts, group = conds) : Calculating library sizes from total number of reads for each library. > dgl <- estimateCommonDisp( dgl ) > res <- exactTest( dgl, c( "A", "C" ) ) Comparison of groups: C - A > sessionInfo() R version 2.11.0 Under development (unstable) (2009-12-17 r50765) i386-pc-mingw32 locale: [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252 [4] LC_NUMERIC=C LC_TIME=English_Australia.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] edgeR_1.5.4 loaded via a namespace (and not attached): [1] limma_3.3.4 > Date: Wed, 16 Dec 2009 19:03:10 +0100 > From: Simon Anders <anders at="" embl.de=""> > Subject: [BioC] edgeR: Contrast selection > To: Mark Robinson <mrobinson at="" wehi.edu.au="">, BioC list > <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <4B2920DE.4020504 at embl.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Mark > > I cannot figure out how to specify which conditions to contrast against > each other in an edgeR exactTest. > > I do the following: > > > library( edgeR ) > > counts <- matrix( rnbinom( 600, 5, .1 ), ncol=6 ) > > conds <- c( "A", "A", "B", "B", "C", "C" ) > > dgl <- DGEList( counts=counts, group=conds ) > Warning message: > In DGEList(counts = counts, group = conds) : > Calculating library sizes from total number of reads for each library. > > dgl <- estimateCommonDisp( dgl ) > > Now I have a DGEList with 6 samples in 3 conditions. If I want to > contrast 'C' vs 'A', I assume I should do > > > res <- exactTest( dgl, c( "A", "C" ) ) > > However, I get this error here: > > Comparison of groups: C - A > Error in Ops.factor(pair[1], group) : level sets of factors are different > > > Have I misunderstood the syntax, or is this a bug? I've tried around a > bit with passing a factor instead, even with all three levels, but this > did not help. > > Thanks in advance for any help. > > Cheers > Simon > > > > sessionInfo() > R version 2.11.0 Under development (unstable) (--) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] edgeR_1.5.3 > > loaded via a namespace (and not attached): > [1] limma_3.3.1 > > > > +--- > | Dr. Simon Anders, Dipl.-Phys. > | European Molecular Biology Laboratory (EMBL), Heidelberg > | office phone +49-6221-387-8632 > | preferred (permanent) e-mail: sanders at fs.tum.de ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}