Hi Krys Kelly wrote: > You could try Tom Hardcastle's baySeq package which allows more complex > designs. There isn't an example of a three group design in the vignette, > but there is one in the draft manuscript which we are about to send off. > Perhaps Tom might email you a copy of this example. Actually, I don't have a more complex design. The main limitation of edgeR is that you cannot form complex contrasts such as an interaction vs the sum of two main effects, or the like. However, having more than two conditions should be possible, provided one always only contrasts one against the other. Actually, I already got a reply by Mark (which somehow did not make it on the list): he is travelling at the moment, but they will look into it very soon. Cheers Simon

Thomas J Hardcastle wrote: > http://www.bioconductor.org/packages/release/bioc/vignettes/baySeq/i nst/doc/baySeq.pdf Hmm, but a little more interesting than that... The 'build report' for baySeq in the release branch http://bioconductor.org/checkResults/2.5/bioc-LATEST/ shows a warning on the windows build machine (liverpool) related to the vignette not being built, and in fact the 'zip' file used to install on Windows does not contain the pdf. This is likely an issue on our build machines here in Seattle, so we'll try and fix this over the next several days. Martin > > > Best, > > Tom > > Naomi Altman wrote: >> I just installed baySeq. Most of the documentation is there, but I >> cannot find the vignette. >> >> --Naomi >> >> >> At 04:38 AM 12/18/2009, Krys Kelly wrote: >>> Hi Simon, >>> >>> You could try Tom Hardcastle's baySeq package which allows more complex >>> designs. There isn't an example of a three group design in the >>> vignette, >>> but there is one in the draft manuscript which we are about to send off. >>> Perhaps Tom might email you a copy of this example. >>> >>> Cheers >>> >>> Krys >>> >>> >>> Dr Krystyna A Kelly (Krys) >>> Bioinformatics Group Leader >>> >>> Department of Plant Sciences >>> University of Cambridge >>> Downing Street >>> Cambridge CB2 3EA >>> United Kingdom >>> >>> Tel: +44 (0)1223 748 969 >>> Fax: +44 (0)1223 333 953 >>> >>> >>> >>> -----Original Message----- >>> From: bioconductor-bounces at stat.math.ethz.ch >>> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Sunny >>> Srivastava >>> Sent: 17 December 2009 23:59 >>> To: Simon Anders >>> Cc: BioC list >>> Subject: Re: [BioC] edgeR: Contrast selection >>> >>> Dear Simon, >>> The last time I used edgeR, it was only supported 2 groups >>> comparisons. As >>> you have three treatment groups, this may be a possible problem. >>> >>> It may be a bug, but it may be also related to the limitation of this >>> package. >>> >>> Hope this helps! >>> >>> Mark, pls correct me if I am wrong. >>> >>> Thanks and Best Regards, >>> S. >>> >>> On Wed, Dec 16, 2009 at 1:03 PM, Simon Anders <anders at="" embl.de=""> wrote: >>> >>> > 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 >>> > >>> > _______________________________________________ >>> > Bioconductor mailing list >>> > Bioconductor at stat.math.ethz.ch >>> > https://stat.ethz.ch/mailman/listinfo/bioconductor >>> > Search the archives: >>> > http://news.gmane.org/gmane.science.biology.informatics.conductor >>> > >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> Naomi S. Altman 814-865-3791 (voice) >> Associate Professor >> Dept. of Statistics 814-863-7114 (fax) >> Penn State University 814-865-1348 (Statistics) >> University Park, PA 16802-2111 >> > > -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793