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rcastelo / GSVA

Gene set variation analysis
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Calling gsva is defunct, use a method-specific parameter object (error) #172

Closed LnOp16 closed 2 months ago

LnOp16 commented 4 months ago

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 commented 4 months ago

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.