creating a heatmap from ExpressionSet

Question

[Shamim Sarhadi]

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?

[Sean Davis]

Are you asking how to make a heatmap from an ExpressionSet, or about how to normalize data from 3 GSE records?

[Shamim Sarhadi]

My dataset is normalized,I want to make a heatmap

Answer 1

[Sean Davis]

# eset is an ExpressionSet
sds = apply(exprs(eset),1,sd)
library(gplots)
# heatmap of the top 100 most variable genes
heatmap.2(exprs(eset)[order(sds,decreasing=TRUE)[1:100],])

Answer 2

[Shicheng Guo]

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.

[Shamim Sarhadi]

Thank you Mr. Shicheng Guo, could you tell me,how I can select differential expression probe in my ExpressionSet?