GSEA error
rdf1993 opened this issue · comments
Warning in RunGSEA(srt = scData.OST.l[[i]], group_by = paste0("Standardpca_SNN_res.", :
All values in the geneScore are greater than zero. Set scoreType = 'pos'.
Species: Homo_sapiens
Loading cached db: GO_BP version:3.14.0 nterm:16029 created:2023-10-24 22:08:40
Permform GSEA...
|=============================================== | 67%
Error: BiocParallel errors
1 remote errors, element index: 4
0 unevaluated and other errors
first remote error: GSEA statistic is not defined when all genes are selected
In addition: Warning message:
stop worker failed:
wrong args for environment subassignment
because of The BiocParallel errors.
If you are using windows, just set register(SnowParam(workers = 1, progressbar = TRUE)).
just use one core
I also set "register(SnowParam(workers = 1, progressbar = TRUE))," but it appears that it's not functioning as expected. I'm curious if there's an alternative method to avoid using the BiocParallel package in this function?
Error: BiocParallel errors
element index: 17, 18, 19, 20, 21, 22, ...
first error: missing value where TRUE/FALSE needed
In addition: There were 12 warnings (use warnings() to see them)