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santos22903
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@santos22903-17230
Last seen 6.0 years ago
Hi, I am trying to do gene set enrichment using MAST. I mostly follow the vignette. Here is the code:
gseaFDR <- 0.05
bootstrapReplicates <- 3# 3 for temp testing - takes too long
module <- "BTM" # seems, the only one they have anyway
packageExt <- system.file("extdata", package='MAST')
module_file <- list.files(packageExt, pattern = module, full.names = TRUE)
gene_set <- getGmt(module_file) # getting GeneSetCollection
gene_ids <- geneIds(gene_set) # extracting gene IDs
print(head(gene_ids))
## gene sets for human genes; to compare with mouse, remove all capitalization
sets_indices <- limma::ids2indices(sapply(gene_ids,tolower), tolower(mcols(scaObj)$symbol))
print(head(sets_indices))
start_time <- Sys.time()
boots <- bootVcov1(zlmCond, R=bootstrapReplicates)
end_time <- Sys.time()
message("\n bootstrapping time ")
print(end_time - start_time)
gsea <- gseaAfterBoot(zlmCond, boots, sets_indices, CoefficientHypothesis("conditionKO"))
z_stat_comb <- summary(gsea, testType='normal')
sigModules <- z_stat_comb[combined_adj<gseaFDR]
When I run the code with 3 repetitions of bootstrapping (bootstrapReplicates <- 3), everything looks fine, but when I run it for real, with 60 bootstrapReplicates, I get a number (7 to be exact) of such warnings:
In .bayesglm.fit.loop.printWarnings(Warning, state, family) : fitted probabilities numerically 0 or 1 occurred
So, I have a few questions:
- Can I trust the fit and consequently the enrichment?
- What are these warnings talking about?
- What, if anything, to do about them?
Thank you.
Can you provide the output from `sessionInfo()`?
Here it is, after running with 3 bootstrapReplicates: