No overlapping genes between markers and bulk.eset

[MobinKhoramjoo]

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

[brandonjew]

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:

bisque/R/marker_based.R

Lines 97 to 101 in 8640250

	GetUniqueMarkers <- function(x, gene_col="gene"){
	keep <- ! (duplicated(x[,gene_col], fromLast = FALSE) |
	duplicated(x[,gene_col], fromLast = TRUE) )
	return(x[keep,])
	}

[MobinKhoramjoo]

Thanks for getting back to me quickly.

I have already tried this but it still does not work!

Do you know any way to be used for mouse data by marker based composition?
I appreciate your time.