Question: 2d- heatmap for RNA-Seq study
0
gravatar for Sujata
2.6 years ago by
Sujata0
india
Sujata0 wrote:

I have two samples and each has biological replicates. I have run Cufflinks, cuffcompare, and then cuffdiff on it. How do I draw a 2d-heatmap from the cuffdiff or cufflinks output?

I would like to use R for it. Any suggestions?

rna-seq next-gen R • 977 views
ADD COMMENTlink modified 2.6 years ago by EagleEye6.3k • written 2.6 years ago by Sujata0

Basically you need to get the FPKM values from cufflinks/cuffdiff in the form of a table/matrix for each sample and replicates. Then you could feed these values to R programs ( e.g ) or cluster3.0

ADD REPLYlink written 2.6 years ago by geek_y9.6k
1
gravatar for seta
2.6 years ago by
seta1.2k
Sweden
seta1.2k wrote:

You can try "pheatmap" package in R for drawing heatmap.

ADD COMMENTlink written 2.6 years ago by seta1.2k
1
gravatar for EagleEye
2.6 years ago by
EagleEye6.3k
Sweden
EagleEye6.3k wrote:

Check out this post,

Heatmaps in R

ADD COMMENTlink written 2.6 years ago by EagleEye6.3k
0
gravatar for hns
2.6 years ago by
hns140
USA/Boston
hns140 wrote:

You could try using CummeRbund which sits well with cuffdiff data and has one line commands to plot heat maps.

ADD COMMENTlink written 2.6 years ago by hns140

I tried using CummeRbund but it doesn't give 2d- heatmaps with dendograms on both sides

ADD REPLYlink written 2.6 years ago by Sujata0
0
gravatar for Ron
2.6 years ago by
Ron930
United States
Ron930 wrote:

Look at gplots package in R. Another tutorial http://sebastianraschka.com/Articles/heatmaps_in_r.html

ADD COMMENTlink written 2.6 years ago by Ron930
0
gravatar for Farbod
2.6 years ago by
Farbod3.2k
Toronto
Farbod3.2k wrote:

Dear Sujata, Hi.

And you can manipulate your heatmap using TM4 MeV.

~ Best

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Farbod3.2k
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