I keep running into the same error:

ssgseaparam <- ssgseaParam(
  expr = TCGA_FPKM_UQ,
  geneSets = converted_gene_sets,
)

gsva_results <- GSVA::gsva(ssgseaparam, verbose = TRUE)

And run into the error: Error in .local(gSets, ...) : unused arguments (minSize = 1, maxSize = Inf) As context, TCGA_FPKM_UQ is a numeric matrix where the row names are the gene IDs and there is no gene id column. Additionally, the converted_gene_sets is a list of enriched KEGG gene sets and their genes from KEGG enrichment analysis. I couldn't find any solutions and I don't know what to do.

Can anyone help? Willing to provide more info if needed. Thanks to anyone in advance!

Hi, here is a good place to ask questions when encountering problems with GSVA.

I cannot reproduce this behaviour with the current release version 2.0.5 and my own test data, so the output of

sessionInfo()

and the original output from

gsva_results <- GSVA::gsva(ssgseaparam, verbose = TRUE)

would help us to help you.

To give us some idea about your input data you could also include the output of, e.g.,

head(TCGA_FPKM_UQ)

and

head(converted_gene_sets)

You should also remove the unnecessary comma (",") after converted_gene_sets, i.e.,

ssgseaparam <- ssgseaParam(
  expr = TCGA_FPKM_UQ,
  geneSets = converted_gene_sets
)

but since I cannot reproduce the issue I don't know if this makes any difference.

It looks like the ssgseaParam function might not be passing the correct parameters to GSVA::gsva(). The error suggests that minSize and maxSize are not recognized in .local(). Try running gsva() directly with your inputs instead of using ssgseaParam, or check if ssgseaParam is compatible with the latest GSVA version. Let me know if you need more help!