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?
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written
by
Shamim Sarhadi
# 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],])
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.
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written
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Shicheng Guo
Thank you Mr. Shicheng Guo, could you tell me,how I can select differential expression probe in my ExpressionSet?
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written
by
Shamim Sarhadi
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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