I've merged 3,GSE from geoDB, and now I have a gene ExpressionSet,is it possible tu create a heatmap from ExpressionSet or I should preprocessing that before I could draw a heatmap?
Are you asking how to make a heatmap from an ExpressionSet, or about how to normalize data from 3 GSE records?
My dataset is normalized,I want to make a heatmap
# eset is an ExpressionSet
sds = apply(exprs(eset),1,sd)
# heatmap of the top 100 most variable genes
You should not do it because the number of probe is to large. The pdf of the heatmap would be come up to 50-100M. I think you need select the differential expression/methylation probes and then do the heatmap.
Tank you MR Shicheng Guo , could you tell me,how I can select differential expression probe in my expressionset?