generating CLS file for GSEA from Cuffdiff output

Question

[onspotproductions]

I have differential expression data generated from cuffdiff that we would like to perform GSEA & GSVA on. I am unsure how to generate a CLS file for use with either of these toolsets. I plan to uses databases from msigDB and gseapy.

Answer 1

[BioNinja]

If you plan to use gseapy, the fastest way is that you can assign a python list object to the parameter cls inside python console like this:

class_verctor = ['KO','KO','KO','WT','WT','WT']

You can see some examples here: http://pythonhosted.org/gseapy/gseapy_example.html