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Cannot convert Seurat object to loom

Open jamiexie opened this issue 5 years ago • 2 comments

Hi the as.loom function is not converting my Seurat object to loom and running into an error message. Is there a reason why this is happening?

> dge_E.loom <- as.loom(dge_Epithelial, filename = "dge_E.loom", verbose = FALSE)
Transposing input data: loom file will show input columns (cells) as rows and input rows (features) as columns
This is to maintain compatibility with other loom tools
Adding: CellID
Adding: Gene
Adding: vst_mean
Adding: vst_variance
Adding: vst_variance_expected
Adding: vst_variance_standardized
Adding: vst_variable
Adding: Selected
Adding: orig_ident
Adding: nCount_RNA
Adding: nFeature_RNA
Adding: percent_mt
Adding: RNA_snn_res_0_8
Error in if (size == Inf) { : missing value where TRUE/FALSE needed

jamiexie avatar Jun 11 '20 23:06 jamiexie

I have the same problem and it is not due to the issue of NA values in metadata column

Crystalizeee avatar Aug 07 '20 08:08 Crystalizeee

I am having the same problem

Manikgarg avatar Sep 02 '20 14:09 Manikgarg