Hi Bioconductor's Users, I found in the list archives a step-by-step for to do a heatmap with a hclust. It is in: http://files.protsuggest.org/biocond/html/1127.html ///I tested it and I modifield it to my code, like this: [1]dist.x <- dist(exprs(todos.norm),method="euclidean",diag=TRUE) clust.x <- hclust(dist.x, method="average") [2]dist.y <- dist(t(exprs(todos.norm)), method="euclidean",diag=TRUE) clust.y <- hclust(dist.y,method="average") heatmap(exprs(todos.norm), Rowv=as.dendrogram(clust.x), Colv=as.dendrogram(clust.y), cexRow=1, cexCol=1,col=greenred.colors(255)) # function greenred is (....). x1 <- exprs(todos.norm[1:50,]) x2 <- exprs(todos.norm[51:100,]) heatmap(x1, cexRow=1, cexCol=1,col=greenred.colors(255)) It works better from normalized data set, but, I would like to run it on eBayes object from limma. Is it possible? I would like to see my all data, because I have a lot off methabolics pathway and we is very curious to see if theses pathways are grouped together. I suppose that is not need to calculate [1]!?? Thanks Marcelo /