gseDo function issue
0
0
Entering edit mode
@02744fb2
Last seen 2.1 years 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 • 1.2k views
ADD COMMENT

Login before adding your answer.

Traffic: 864 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