Error in running: classifySingleR from SingleR package
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@194e4677
Last seen 4 days ago
Israel

I'm trying to run classifySingleR function from SingleR package using MouseRNAseqData() as a reference to classify the cells from a Seurat dataset that has not yet been published, but I got the following error:

Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'colRanks': error in evaluating the argument 'seed' in selecting a method for function 'DelayedArray': invalid or not-yet-implemented 'Matrix' subsetting


library(SingleR)

df_genes <- readRDS("Seuratfile.rds")
mrnaseq <- MouseRNAseqData()
test <- df_genes@assays$RNA@data # a Seurat dataset
shared_markers <- row.names(mrnaseq)[row.names(mrnaseq)%in%row.names(test)] # shared markers in the reference and in our gene expression data
sub_test <- test[shared_markers,]

singler_out <- classifySingleR(test = sub_test, trained = mrnaseq) 

sessionInfo( )
SingleR SingleCell • 65 views
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You do not include your sessionInfo. Be sure to use the latest version, there have been changes towards DelayedArray support it seems (https://bioconductor.org/packages/release/bioc/news/SingleR/NEWS) maybe it's simple a version issue.

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