Ahh thanks for your reply Mark, I had atempted this yesterday using row means of the treatment.. but was of course still getting a mix of up and down as I wasn't accounting for the expression level in the control. Looks great now. Cheers Alice -----Original Message----- From: Mark Cowley [mailto:m.cowley0@gmail.com] Sent: Wednesday, 25 June 2008 8:12 p.m. To: Johnstone, Alice Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] row clustering in heatmap.2 Hi Alice, From the help page (?heatmap.2): Rowv: determines if and how the _row_ dendrogram should be reordered. By default, it is TRUE, which implies dendrogram is computed and reordered based on row means. If NULL or FALSE, then no dendrogram is computed and reordering is done. If a 'dendrogram', then it is used "as-is", ie without any reordering. If a vector of integers, then dendrogram is computed and reordered based on the order of the vector. 1) reorder the rows before you put it into the heatmap.2 see ?order 2) turn row-reordering off in the heatmap by using heatmap.2 with Rowv=FALSE, Colv=TRUE, dendrogram="column" if you want the columns reordered, or Rowv=FALSE, Colv=FALSE, dendrogram="none" for neither row or column dendrograms cheers, mark On 25/06/2008, at 12:49 PM, Johnstone, Alice wrote: > Hi > Im having a hard time trying to understand the clustering functions > used with heatmap.2. I have expression data, treatment vs control for > which I have created a heatmap for (default arguments). But I want to > reorder the rows so that the row with the highest expression in my > treatment is at the top, the 2nd having the 2nd highest > expression..etc.. down to the last row having the lowest expression > (compared to the control). > Any suggestions on how I can go about this would be very much > appreciated! > Thank you > > Alice Johnstone > > PhD Student > Institute of Environmental Science and Research Ltd Kenepuru Science > Centre > 34 Kenepuru Drive > PO Box 50-348 > Porirua > New Zealand > > Tel: + 64 4 914-0717 > Fax: + 64 4 914-0770 > > > P Think before you print > This e-mail transmission and any attachments that accompany it may > contain information that is privileged, confidential or otherwise > exempt from disclosure under applicable law and is intended solely for > the use of the individual(s) to whom it was intended to be addressed. > If you have received this e-mail by mistake, or you are not the > intended recipient, any disclosure, dissemination, distribution, > copying or other use or retention of this communication or its > substance is prohibited. If you have received this communication in > error, please immediately reply to the author via e-mail that you > received this message by mistake and also permanently delete the > original and all copies of this e-mail and any attachments from your > computer. Thank you. > > _______________________________________________ > 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