I have used the functions described in the DEseq package information for clustering and heatmap visualization of RNA-seq data with great results. However I am a bit confused whether I may be able to use the conds argument for my count dataset. When I have replicate samples I would like to get only the ones specified in the conds vector as the nodes in the dendrogram of the heatmap. Is this possible to do using methods in the DEseq package or do I have to calculate average values for the replicates manually before I obtain the distances? -- output of sessionInfo(): -- Sent via the guest posting facility at bioconductor.org.

Dear Linn each sample's data corresponds to a column in the data matrix of a countDataSet, and it seems that your question boils down on how to 1. subset columns of a matrix 2. compute average vector from sets of columns of a matrix. For 1., you can do something like library(Biobase) library(pasilla) data(pasillaGenes) s1 = pasillaGenes[, pasillaGenes$type=="single-read"] For 2., see the 'ave' function in the 'stats' package, or more pedestrian: sp = with(pData(pasillaGenes), split(seq(along=condition), condition)) mn = do.call(cbind, lapply(sp, function(i) rowMeans(vsd[,i,drop=FALSE]))) where 'vsd' is the data after variance stabilising transformation as described in the vignette. Best wishes Wolfgang Nov/10/11 1:45 PM, Linn Fagerberg [guest] scripsit:: > > I have used the functions described in the DEseq package information > for clustering and heatmap visualization of RNA-seq data with great > results. However I am a bit confused whether I may be able to use the > conds argument for my count dataset. When I have replicate samples I > would like to get only the ones specified in the conds vector as the > nodes in the dendrogram of the heatmap. Is this possible to do using > methods in the DEseq package or do I have to calculate average values > for the replicates manually before I obtain the distances? > > -- output of sessionInfo(): > > > > -- Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ Bioconductor mailing > list Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber