Question: creating a heatmap from ExpressionSet
2
gravatar for Shamim Sarhadi
4.3 years ago by
IRAN
Shamim Sarhadi210 wrote:

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?

R • 1.8k views
ADD COMMENTlink modified 4.3 years ago by Sean Davis25k • written 4.3 years ago by Shamim Sarhadi210

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

ADD REPLYlink written 4.3 years ago by Sean Davis25k

My dataset is normalized,I want to make a heatmap

ADD REPLYlink written 4.3 years ago by Shamim Sarhadi210
4
gravatar for Sean Davis
4.3 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:
# 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],])

ADD COMMENTlink written 4.3 years ago by Sean Davis25k
1
gravatar for Shicheng Guo
4.3 years ago by
Shicheng Guo7.8k
Shicheng Guo7.8k wrote:

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.

ADD COMMENTlink written 4.3 years ago by Shicheng Guo7.8k

Tank you MR Shicheng Guo , could you tell me,how I can select differential expression probe in my expressionset?

ADD REPLYlink written 4.2 years ago by Shamim Sarhadi210
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1269 users visited in the last hour