2d- heatmap for RNA-Seq study

Question

[Sujata]

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?

[GouthamAtla]

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

Answer 1

[seta]

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

Answer 2

[EagleEye]

Check out this post,

Heatmaps in R

Answer 3

[hns]

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

[Sujata]

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

Answer 4

[Ron]

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

Answer 5

[Farbod]

Dear Sujata, Hi.

And you can manipulate your heatmap using TM4 MeV.

~ Best