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Adrian, Starting from your list of significant genes: :> library(simpleaffy) :> library(bioDist) :> pdf(file="heatmap.pdf",height=8, width=8) :> heatmap(exprs(data.rma)[my.list,], col=blue.white.red.cols, distfun=euc, hclustfun=function(c){hclust(c,method='average')}) :> dev.off() David On Apr 1, 2008, at 2:44 AM, Adrian Johnson wrote: > dear list: > > I finished a LIMMA analysis for two color Agilent 4x44 arrays. I > found 800 > genes (my choice of fold change under -2 and over +2) at 5%FDR. > > I have 30 normal(cy3) and cancer (cy5) samples (paired design). > > how can I do clustering and make heatmap after getting significant > genes > (eBayes(lmfit) step). > > Appreciate your help. thanks > Ad. > > [[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