search

rcastelo / GSVA

Gene set variation analysis
200 stars 40 forks source link

Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct #213

Open lucyu2668 opened 2 hours ago

lucyu2668 commented 2 hours ago

example(gsva) es <- gsva(y, geneSets) Error: gsva(y, geneSets): Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').

My R version is 4.4.1, and GSVA 1.52.3

How to solve the problem?

axelklenk commented 2 hours ago

From https://github.com/rcastelo/GSVA/issues/172

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 es <- gsva(y, geneSets) all you need to do is change it to es <- gsva(gsvaParam(y, geneSets))

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.