Open lucyu2668 opened 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.
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?