Warning in bayes fit in MAST GSEA
0
0
Entering edit mode
@santos22903-17230
Last seen 4.9 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.

MAST GSEA bayesglm.fit • 1.4k views
ADD COMMENT
0
Entering edit mode

Can you provide the output from `sessionInfo()`?

ADD REPLY
0
Entering edit mode

Here it is, after running with 3 bootstrapReplicates:

> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils    
[7] datasets  methods   base     

other attached packages:
 [1] GSEABase_1.40.1            graph_1.56.0              
 [3] annotate_1.56.2            XML_3.98-1.16             
 [5] data.table_1.11.4          limma_3.34.9              
 [7] org.Mm.eg.db_3.5.0         AnnotationDbi_1.40.0      
 [9] SingleCellExperiment_1.0.0 MAST_1.4.1                
[11] SummarizedExperiment_1.8.1 DelayedArray_0.4.1        
[13] matrixStats_0.54.0         Biobase_2.38.0            
[15] GenomicRanges_1.30.3       GenomeInfoDb_1.14.0       
[17] IRanges_2.12.0             S4Vectors_0.16.0          
[19] BiocGenerics_0.24.0       

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.4       purrr_0.2.5           
 [3] reshape2_1.4.3         lattice_0.20-35       
 [5] colorspace_1.3-2       blob_1.1.1            
 [7] rlang_0.2.2            pillar_1.3.0          
 [9] glue_1.3.0             DBI_1.0.0             
[11] bit64_0.9-7            bindrcpp_0.2.2        
[13] GenomeInfoDbData_1.0.0 plyr_1.8.4            
[15] bindr_0.1.1            stringr_1.3.1         
[17] zlibbioc_1.24.0        munsell_0.5.0         
[19] gtable_0.2.0           memoise_1.1.0         
[21] Rcpp_0.12.18           xtable_1.8-3          
[23] scales_1.0.0           XVector_0.18.0        
[25] abind_1.4-5            bit_1.1-14            
[27] ggplot2_3.0.0          digest_0.6.16         
[29] stringi_1.2.4          dplyr_0.7.6           
[31] grid_3.4.4             tools_3.4.4           
[33] bitops_1.0-6           magrittr_1.5          
[35] lazyeval_0.2.1         RCurl_1.95-4.11       
[37] tibble_1.4.2           RSQLite_2.1.1         
[39] crayon_1.3.4           pkgconfig_2.0.2       
[41] Matrix_1.2-14          assertthat_0.2.0      
[43] R6_2.2.2               compiler_3.4.4 
ADD REPLY

Login before adding your answer.

Traffic: 855 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6