Can anyone help me with this script error?

Question

[nuorain]

Hi, I tried to run this code but encounter the error.

gsva_matrix<- gsva(as.matrix(tcga_exp), gene_set,
                   method='ssgsea',kcdf='Gaussian',abs.ranking=TRUE)

Error in gsva(as.matrix(tcga_exp), gene_set, method = "ssgsea", kcdf = "Gaussian",  : 
  Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').

Can anyone help me out? Thank you very much. Best J

[aUser]

Which version you are using? As per the documentation, the authors change the API, so you need different command; e.g:

gsvaParam(
exprData,
geneSets,
assay = NA_character_,
annotation = NULL,
minSize = 1,
maxSize = Inf,
kcdf = c("auto", "Gaussian", "Poisson", "none"),
kcdfNoneMinSampleSize = 200,
tau = 1,
maxDiff = TRUE,
absRanking = FALSE,
sparse = TRUE,
checkNA = c("auto", "yes", "no"),
use = c("everything", "all.obs", "na.rm")
)

Look into the documentation. https://www.bioconductor.org/packages/release/bioc/manuals/GSVA/man/GSVA.pdf

[nuorain]

Hi, thank you for your reply. I am using version 2.0.1. I solved the problem by converting gene_set to gmt file.