Cufflinks output - how to produce heatmap of diff exp genes as z-scores

Question

[tahneesaunders]

Hi all,

I have performed followed the Tophat alignment and Cufflinks differential analysis pipelines for my RNAseq data. I am not playing around in R with Cummerbund - I can produce pretty nice volcano plots and extract lists of significant genes.

I was wondering what the best way to produce a heatmap of z-scores using the cufflinks output is?

Appreciate all your suggestions.

Thanks. Tahnee.

(I have searched for about an hour to find an 'easy' solution, however cannot find one to my skill level, without being an R expert...).

Answer 1

[Kevin Blighe]

Hi, you may want to take a look at my answer here, where I have done specifically this: Heatmap based with FPKM values

You will have to get your data in this format:

      Sample1 Sample2 Sample3 Sample4 ...
Gene1 45      453       2       4
Gene2 45       43     444      53
Gene3 40        3      23     232
Gene4 50       56      43     224
...

Answer 2

[domenico.somma]

Hello, I wrote a python module named Papillon for this purpose. Python normally is easier to learn than R. You can find Papillon here. There is a tutorial, you can install it with pip or conda, and make a heatmap is very easy:

import papillon as pp

MyExp=pp.read_db("My Experiment")                # "My Experiment" is the folder name of your data

MyExp.get_gene()             # you can select gene/isoform o specific gene name (see the tutorial)

MyExp.heatmap(z_score=True)

Best Regards Dom