Hi All

I am trying to use R (RStudio 2024.12.1+563 "Kousa Dogwood" Release) to do GSVA analysis. I have created the datasets of RNA Seq count data and gene set (I tried using .txt Tab Delimited, .csv, and excel format). However, when trying to run the code, I keep getting these error message:

Error in gsva(expr = as.matrix(rna_seq_sub), gset.idx.list = gene_set_list,  : 
  Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').

Error in gsvaParam(exprsData = as.matrix(rna_seq_sub), gset.idx.list = gene_set_list,  : 
  unused arguments (exprsData = as.matrix(rna_seq_sub), gset.idx.list = gene_set_list, method = "gsva")

I tried to reinstall the GSVA several times using this command I got from https://bioconductor.org/packages/release/bioc/html/GSVA.html but it seemed the error persist.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("GSVA")

Has anybody encounter similar problem? Looking forward for your suggestion. Thank you very much for your help!

Please go through the current vignette to learn about the syntax and functions. There were quite drastic changes recently, so older code will not work anymore. For example, gsvaParam() now needs to be defined before calling gsva() itself. See vignette.