The consensusTMEAnalysis() function no longer works with R version 4.4.0, Bioconductor release 3.19. Particularly the function geneSetEnrichment() fails because the previous GSVA API is defunc:
Error in GSVA::gsva(expr = bulkExp, gset.idx.list = signatures, method = statMethod, : Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').
Hi, thank you for this beautiful package!
The consensusTMEAnalysis() function no longer works with R version 4.4.0, Bioconductor release 3.19. Particularly the function geneSetEnrichment() fails because the previous GSVA API is defunc:
Error in GSVA::gsva(expr = bulkExp, gset.idx.list = signatures, method = statMethod, : Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').as you can see also here: https://github.com/rcastelo/GSVA/issues/172
Would it be possible to update the ConsensusTME package to accommodate the newest Bioconductor release? Thank you!