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2d- heatmap for RNA-Seq study

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 r next-gen
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updated by EagleEye EagleEye • written by Sujata • Sujata

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

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written by GouthamAtla GouthamAtla

5 answers

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

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written by seta seta

Check out this post,

Heatmaps in R

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written by EagleEye EagleEye

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

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written by hns hns

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

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written by Sujata • Sujata

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

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written by Ron Ron

Dear Sujata, Hi.

And you can manipulate your heatmap using TM4 MeV.

~ Best

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written by Farbod Farbod

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