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Cannot convert Seurat object to loom #65

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jamiexie opened this issue Jun 11, 2020 · 2 comments
Open

Cannot convert Seurat object to loom #65

jamiexie opened this issue Jun 11, 2020 · 2 comments

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@jamiexie
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jamiexie commented Jun 11, 2020

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

@Manikgarg
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I am having the same problem

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