I am using R version 4.2.0. I have a problem when I am running xCell analysis of RNA-seq data. I tried the
rawEnrichmentAnalysis(data, xCell.data$signatures, xCell.data$genes, parallel.sz = 4, parallel.type = "SOCK")
(it also happened in xCellAnalysis), then I got this error:
ERROR: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
I also used IOBR and immunedeconv packages after updated all the packages, both of them gave me the same error(cibersort and EPIC worked well, but I really need the result of xCell).
I think this problem is caused by GSVA package. Could anyone please help me with this? Thank you very much!!