Inconsistency of results GSEA clusterprofiler
0
0
Entering edit mode
Stane ▴ 40
@stane-10974
Last seen 6.2 years ago

Hello, 

I have been trying to reproduce results from gsea using clusterprofiler and gseKEGG

(for some unknow reason gseGO is not working for me )

simply repeating experiment on the same gene expression data about 13k genes: 

 gseKEGG(geneList = zscores,
                      organism = 'hsa',
                      nPerm = 1000,
                      pvalueCutoff = 0.05,
                      verbose = F)

about 80% of the time I am getting 0 gene set enrichment and the other 20% I am getting approximatively the same 8-9 gene sets. I have to compute gene set for about 400k assays and would like to make sure I can get consistent results. 

I understand that some parts of the process use some random number but I find strange that I am getting gene set enrichment only 20% of the time with the exact same data. 

I could implement a loop to repeat the experiment until I am getting results for each assay but is there any other method which I may not be aware of directly in the package? Or another package that you guys would recommend instead of clusterprofiler? 

Best 

 

gsea clusterprofiler • 1.7k views
ADD COMMENT
1
Entering edit mode

I just bumped the nPerm to 5k and now the results seems more consistent

ADD REPLY

Login before adding your answer.

Traffic: 808 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6