Search
Question: Inconsistency of results GSEA clusterprofiler
0
gravatar for Stane
6 days ago by
Stane40
Stane40 wrote:

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 

 

ADD COMMENTlink written 6 days ago by Stane40
1

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

ADD REPLYlink written 6 days ago by Stane40
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 266 users visited in the last hour