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.