Hi, I just came across the latest update on the vignette of "DESeq". I really like the new additions on visualizations particularly the visualization of expression data from genes. In my rna-seq experiment I have two conditions/treatments and three biological replication per treatment. I did the differential expression analysis and variance stabilized data using "DESeq". I want to use the VSD for generating heat map of top DE genes. I am using heatmap.2. I am able to generate a good heat map. However , I want to place an horizontal bar (below the vertical dendrogram) using 'ColSideColors' function of heat map2. I have generated the heatmap with the dendrogram of sample data (three biological replicates ie C1,C2,C3,S1,S2,S3; C=control; S=stress) on the top (vertical) of map. On the horizontal bar (below the vertical dendrogram) I want to have two colours one for each of the two treatments. I am able to add one colour to each sample using 'rainbow' and 'heat.colors' functions but I want to use only two colours one for each of the two conditions. Could anyone please show me how to do this. Thank you. Bala [[alternative HTML version deleted]]

Bala have a look at this very nice page: http://www2.warwick.ac.uk/fac/sci/moac/students/peter_cock/r/heatmap (It can be found by typing "heatmap.2 colsidecolors" into Google.) Wolfgang. Il May/12/11 8:20 AM, Reddy.Thumma at csiro.au ha scritto: > Hi, > I just came across the latest update on the vignette of "DESeq". I really like the new additions on visualizations particularly the visualization of expression data from genes. In my rna-seq experiment I have two conditions/treatments and three biological replication per treatment. I did the differential expression analysis and variance stabilized data using "DESeq". I want to use the VSD for generating heat map of top DE genes. I am using heatmap.2. I am able to generate a good heat map. However , I want to place an horizontal bar (below the vertical dendrogram) using 'ColSideColors' function of heat map2. I have generated the heatmap with the dendrogram of sample data (three biological replicates ie C1,C2,C3,S1,S2,S3; C=control; S=stress) on the top (vertical) of map. On the horizontal bar (below the vertical dendrogram) I want to have two colours one for each of the two treatments. I am able to add one colour to each sample using 'rainbow' and 'heat.colors' functions bu t! > I want to use only two colours one for each of the two conditions. > > Could anyone please show me how to do this. > > Thank you. > Bala > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber