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zhanghao-njmu / SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
https://zhanghao-njmu.github.io/SCP/
GNU General Public License v3.0
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GSEA error #212

Open rdf1993 opened 10 months ago

rdf1993 commented 10 months ago

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

christophechu commented 8 months ago

because of The BiocParallel errors. If you are using windows, just set register(SnowParam(workers = 1, progressbar = TRUE)). just use one core

EhsanRz commented 4 months ago

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)