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Dataset distribution for Seurat
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subset pubmc.atac error message using sample data provided by seurat #44

Open sunliang3361 opened 2 years ago

sunliang3361 commented 2 years ago

can anyone help out here? Thank you.

pbmc.atac <- LoadData("pbmcMultiome", "pbmc.atac") the condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be used

repeat QC steps performed in the WNN vignette

pbmc.rna <- subset(pbmc.rna, seurat_annotations != "filtered") pbmc.atac <- subset(pbmc.atac, seurat_annotations != "filtered") Error in vapply(X = keyed.objects, FUN = function(x) { : values must be length 1, but FUN(X[[1]]) result is length 0

timoast commented 2 years ago

See https://github.com/timoast/signac/issues/872#issuecomment-995845779

sunliang3361 commented 2 years ago

thank you for your response. I am actually using SeuratObject_4.0.4. do you know what other potential reasons for my problem? See below:

other attached packages: [1] cowplot_1.1.1 ggplot2_3.3.5 EnsDb.Hsapiens.v86_2.99.0
[4] ensembldb_2.12.1 AnnotationFilter_1.12.0 GenomicFeatures_1.40.1
[7] AnnotationDbi_1.50.3 Biobase_2.48.0 GenomicRanges_1.40.0
[10] GenomeInfoDb_1.24.2 IRanges_2.22.2 S4Vectors_0.26.1
[13] BiocGenerics_0.34.0 Signac_1.5.0 SeuratObject_4.0.4
[16] Seurat_4.0.5 pbmcMultiome.SeuratData_0.1.2 SeuratData_0.2.1