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?