Hi,

I am trying to run PLAGE from the GSVA R package for some single cell pathway analysis. I tried running the script on my local laptop and AWS but encounter the same error. Once it starts "estimating PLAGE scores for 4 gene sets" it starts a progress bar at 0% but then gets killed. Any help would be appreciated!

Code should be placed in three backticks as shown below

```gene_sample_matrix <- rawData[["RNA"]]@data exSet <- ExpressionSet(as.matrix(gene_sample_matrix)) c2_gene_sets <- msigdbr(species = "human", category = "C2") plage <- gsva(exSet, c2_gene_sets, method = "plage")

include your problematic code here with any corresponding output

please also include the results of running the following in an R session

sessionInfo( )

``` R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.3 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale: [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] compiler_4.1.2

hi,

as I understand, you're working with just 4 gene sets, which seems very little, but what are the dimensions of you expression data set?

PLAGE runs quickly in my laptop with 4 gene sets, and an expression data set of 20000 genes by 1000 samples.