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subsetting the gene list
2 messages · Abhilash Venu, Adaikalavan Ramasamy
Have you tried reading some of the material from the BioConductor workshop http://bioconductor.org/workshops/ ? Here is a simplistic way of proceeding: ## Calculate pvalues from t-test p <- apply( mat, function(x) t.test( x ~ cl )$p.value ) ## Subset mat.sub <- mat[ p, ] ## Cluster heatmap(m) Regards, Adai
Abhilash Venu wrote:
Hi all, I am working on a single color expression data using limma. I would like to perform a cluster analysis after selecting the differentially genes based on the P value (say 0.001). As far as my knowledge is concerned I have to do the sub setting of these selected genes on the normalized data (MA), to retrieve the distribution across the samples. But I am wondering whether I can perform using the R script? I would appreciate any help.