gseDo function issue
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@02744fb2
Last seen 18 months ago
United States

I am trying do a GSEA analysis. Here is the code that I have been trying to use.


edo2 <-gseDO(geneList=geneList, 


             minGSSize = 3, 
             maxGSSize = 800, 
             pvalueCutoff = 0.05, 
             verbose = TRUE, 

             pAdjustMethod = "none")

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )

I get following error code. preparing geneSet collections... GSEA analysis... Error: BiocParallel errors 2 remote errors, element index: 1, 30 55 unevaluated and other errors first remote error: Error in fgseaMultilevelCpp(x[, ES], stats, unique(x[, size]), sampleSize, : could not find function "fgseaMultilevelCpp" In addition: Warning messages: 1: In preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (18.78% of the list). The order of those tied genes will be arbitrary, which may produce unexpected results. 2: In serialize(data, node$con) : 'package:stats' may not be available when loading 3: In serialize(data, node$con) : 'package:stats' may not be available when loading

Can some one help me with this? Thank you, Meet

Biocpa BiocParallel • 1.0k views
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