Oops, I take that back. The image is different now that I look at it more closely (they are very similar). However, the original question remains - how do I stop it from reordering the columns? Dave. -----Original Message----- From: Dave Waddell [mailto:dwaddell@nutecsciences.com] Sent: Monday, November 03, 2003 9:54 AM To: Bioconductor Subject: heatmap() column ordering I have four experiments (two dye swaps) and this is the original order: > colnames(mav) [1] Cy3="Cancer" Cy5="Normal" Cy3="Cancer" Cy5="Normal" Cy3="Normal" Cy5="Cancer"Cy3=" Normal" Cy5="Cancer" I want to get a heatmap of the top 30 expressed genes but ordered by cancerous vs. normal tissue. > hv <- heatmap(mav[genes %in% topgenes$Name,],col=RGcol) > title("Heatmap of Top 30 genes") > str(hv) List of 2 $ rowInd: int [1:30] 5 8 30 13 7 27 19 21 25 26 ... $ colInd: int [1:8] 4 3 8 7 1 5 2 6 No matter what I do, the columns are reordered. Furthermore, if I set Colv=F the heatmap stays the same but the ordering changes. > hv <- heatmap(mav[genes %in% topgenes$Name,],col=RGcol,Colv=F) > title("Heatmap of Top 30 genes") > str(hv) List of 2 $ rowInd: int [1:30] 5 8 30 13 7 27 19 21 25 26 ... $ colInd: int [1:8] 3 4 7 8 2 6 1 5 Am I missing something or is this a bug/feature? BTW, is there any way to post images to this group? It seems this would be desirable. Dave Waddell