Is there a way to group samples and display them on an heatmap? Im using the simpleaffy package to analyze some Affymetrix data - we have 12 chips, 6 from each donor (A and B) at different time points / treatments. Im using hmap.pc to build an heatmap out of a filtered paircomp object, but would want to display the mean of the 2 donors for each treatment / time pair (so 6 samples total) instead of each chip on the heatmap. Can this be done?

Hi Michael, Michael Imbeault wrote: > Is there a way to group samples and display them on an heatmap? Im using > the simpleaffy package to analyze some Affymetrix data - we have 12 > chips, 6 from each donor (A and B) at different time points / treatments. > > Im using hmap.pc to build an heatmap out of a filtered paircomp object, > but would want to display the mean of the 2 donors for each treatment / > time pair (so 6 samples total) instead of each chip on the heatmap. > > Can this be done? I can't speak for hmap.pc, as I don't know what package that is in. However you could use either heatmap or heatmap.2 in the gplots package to do the heatmap, in which case you would simply compute the mean of the samples and feed that as input to the heatmap function. Presumably you would be able to do the same for hmap.pc, but as I mentioned, I don't know that function. Best, Jim > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826