GSVA error
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Alex • 0
@6c5a834f
Last seen 5 weeks ago
United Kingdom

Hi All

Hope someone can help as it seems GSVA has some issues with other packages (that likely have been updated).

After running the test code below, an error is thrown "Error: [matrixStats (>= 1.2.0)] useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE. See also ?matrixStats::matrixStats.options"

could someone provide insights into potential fixes?

test code

p <- 10000
n <- 1000
sizeGeneSets <- sample(5:500, size=186, replace=TRUE) geneSets <- lapply(as.list(sizeGeneSets), sample, x=paste0("g", 1:p), replace=FALSE) names(geneSets) <- paste0("gs", 1:length(geneSets)) y <- matrix(rnorm(n*p), nrow=p, ncol=n, dimnames=list(paste("g", 1:p, sep="") , paste("s", 1:n, sep=""))) dim(y)

library(GSVA) gsva_es <- gsva(y, geneSets, parallel.sz=2)

sessionInfo( )

R version 4.2.2 (2022-10-31)

GSVA_1.46.0

```

GSVA • 850 views
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Entering edit mode
Robert Castelo ★ 3.3k
@rcastelo
Last seen 1 day ago
Barcelona/Universitat Pompeu Fabra

Hi,

That error originates in an upstream dependency of GSVA, in matrixStats, concretely after the argument use.names=NA became defunct on December, 11th, 2023 (see here). The solution is to update to the latest release of GSVA and Bioconductor, see https://bioconductor.org/install for details on how to do this.

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Thank you, Robert! The update sorted everything out.

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