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cozygene / bisque

An R toolkit for estimation of cell composition from bulk expression data
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No overlapping genes between markers and bulk.eset #42

Open MobinKhoramjoo opened 1 month ago

MobinKhoramjoo commented 1 month ago

Hello,

I have been trying to run this function for my data. I have faced with this error: " Getting unique markers Error in BisqueRNA::MarkerBasedDecomposition(bulk.eset = bulk, markers = markers, : No overlapping genes between markers and bulk.eset"

I have already checked the overlapping genes in both markers and bulk.eset. There are actually 71 genes overlapping. but this still does not work?

I appreciate your help Screenshot 2024-07-19 142215

brandonjew commented 1 month ago

Hi @MobinKhoramjoo, thank you for your interest in our method! This may be due to the "unique_markers" option. Enabling this option will remove any marker genes that show up in multiple cell types which may remove any overlapping genes. This is different than unique(markers$gene). The function used for this filter is here: https://github.com/cozygene/bisque/blob/8640250dff0b103919518ee78b2a3ea536e830a7/R/marker_based.R#L97-L101

MobinKhoramjoo commented 1 month ago

Thanks for getting back to me quickly.

I have already tried this but it still does not work! Screenshot 2024-07-19 151948 Do you know any way to be used for mouse data by marker based composition? I appreciate your time.