Hello, How do I plot a heatmap of 110 samples with 3200 genes that have been clustered already in R. I tried heatmap2, it works but the plot has white dots on it and it does now show the data like it does in Cluster 3. When I looked into it I found other software doesn't plot such big samples because of memory. So does anyone know for example how to use affy() library image to plot a heatmap of 110x3200 matrix using clustered Ruppert _________________________________________________________________ Celeb spotting ? Play CelebMashup and win cool prizes

Hi Ruppert, if I get you right you have an ExpressionSet for which both rows and columns have been rearranged according to some clustering. So why not do something like image(t(exprs(foo))) As for the dots: are there any NA values in your data? My first guess is that those are your white dots Florian On 13.11.2007, at 21:30, Ruppert Valentino wrote: > > Hello, > How do I plot a heatmap of 110 samples with 3200 genes > that have been clustered already in R. I tried heatmap2, it works > but the plot has white dots on it and it does now show the data > like it does in Cluster 3. When I looked into it I found other > software doesn't plot such big samples because of memory. So does > anyone know for example how to use affy() library image to plot a > heatmap of 110x3200 matrix using clustered > > Ruppert > > > _________________________________________________________________ > Celeb spotting ? Play CelebMashup and win cool prizes > > _______________________________________________ > 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

Dear Ruppert, for plotting large matrices, such as s=sin(seq(-10, 10, length=1000)) a=outer(s,s) try: library("EBImage") display(Image(a)) this is bitmap-based and avoids the vector-drawing costs of 'image'. There is also 'writeImage' to save an Image object directly to a variety of file formats. This is straightforward for greyscale images only. To get colour, you would have to manage the colormap and the conversion into RGB coordinates yourself. Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber Valentino ha scritto: > Hello, > How do I plot a heatmap of 110 samples with 3200 genes that have been clustered already in R. I tried heatmap2, it works but the plot has white dots on it and it does now show the data like it does in Cluster 3. When I looked into it I found other software doesn't plot such big samples because of memory. So does anyone know for example how to use affy() library image to plot a heatmap of 110x3200 matrix using clustered > > Ruppert > >