There are no common gene names in spatial count data and single cell RNAseq count data

[krigia]

@YingMa0107 @YMalab

I am getting the following error

**_QC on scRNASeq dataset! ...

QC on spatially-resolved dataset! ...

Error: There are no common gene names in spatial count data and single cell RNAseq count data_**

Although there are common genes:

Filter datasets to include only common genes

sc_count_Dong_filtered <- sc_count_Dong[common_genes, ] spatial_count_dgCMatrix_filtered <- spatial_count_Giotto_F2_dgCMatrix[common_genes, ] print(length(common_genes)) [1] 15129

common_features <- rownames(sc_count_Dong)[rownames(sc_count_Dong) %in% rownames(spatial_count_Giotto_F2_dgCMatrix)] sc_count_Dong_filtered <- sc_count_Dong[common_features,] sc_count_Dong_filtered <- sc_count_Dong[common_features,] spatial_count_Giotto_F2_dgCMatrix_filtered <- spatial_count_Giotto_F2_dgCMatrix[common_features, ]

print(dim(sc_count_Dong_filtered)) [1] 15129 19372

print(dim(spatial_count_Giotto_F2_dgCMatrix_filtered)) [1] 15129 4955

I would greatly appreciate your input. Thank you.