GSVA problem in TCGAplot

tjhwangxiong / TCGAplot

A number of functions were generated to perform pan-cancer DEG analysis, correlation analysis between gene expression and TMB, MSI, TIME, and promoter methylation. Methods for visualization were provided in order to easily perform integrative pan-cancer multi-omics analysis.

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Hi Xiong,

Thank you for writing this useful tools. I have tried plenty of functions in your package, and most of them worked smoothly. however, for gene set analysis which requries GSVA, such as gs_TMB_radar, gs_boxplot, I ran into this following issue: Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').

my R is 4.4.0, and GSVA is 1.52.2. it seems the new version of GSVA no longer uses GSVA::gsva, that's my guess.

could you please provide a solution for this issue?

Thanks,

Gloria

tjhwangxiong / TCGAplot

GSVA problem in TCGAplot #16