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

[LnOp16]

R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64

[axelklenk]

Thanks for using GSVA.

The previous API of GSVA has been changed to make use of parameter objects and, as the message says, is now defunct after a full release cycle of deprecation. If previously you have used gsva_es <- gsva(as.matrix(gsym.expr), gs) all you need to do is change it to gsva_es <- gsva(gsvaParam(as.matrix(gsym.expr), gs))

For more information about the new API, please do as the message says and see ?gsva or the vignette at https://bioconductor.org/packages/release/bioc/vignettes/GSVA/inst/doc/GSVA.html

Please don't hesitate to let us know if that doesn't solve the issue.