Extremely high contamination estimated (0.61)

[mibdx-dev]

Hi,

I am getting the same error with one my Sample "Error in setContaminationFraction(sc, exp(coef(sc$fit)), forceAccept = forceAccept) : Extremely high contamination estimated (0.61). This likely represents a failure in estimating the contamination fraction. Set forceAccept=TRUE to proceed with this value."

Thea autoEstCont looks very different. I am using only one gene set nonExpressedGeneList = list(Hep=c("CYP1A2","CYP2E1","CYP3A4","GLUL","DCXR","FTL","GPX2","GSTA1","CYP2A7","FABP1","HAL","AGT","ALDOB","SDS"))

Interestingly the same Sample works when I am using a big geneset of which this one is part as well. Hep geneset is part of the lists below as well. However with these list some other samples fail.

nonExpressedGeneList = list(
AntiB=c("IGKC","JCHAIN","IGHA1","IGLC1","IGLC2","IGLC3"),
MatB=c("CD22","CD37","CD79B","FCRL1","LTB","DERL3","IGHG4"),
CD3T=c("CD8A","CD8B","CD3D","CD3G","TRAC","IL32","TRBC1","TRBC2"),
Hep=c("CYP1A2","CYP2E1","CYP3A4","GLUL","DCXR","FTL","GPX2","GSTA1","CYP2A7","FABP1","HAL","AGT","ALDOB","SDS"),
LSEC=c("FCN2","CLEC1B","CLEC4G","PVALB","S100A13","GJA5","SPARCL1","CLEC14A","PLVAP","EGR3"),
Eryth=c("HBB","HBA1","HBA2"),
NKT=c("CSTW","IL7R","GZMB","GZMH","TBX21","HOPX","PRF1","S100B","TRDC","TRGC1","TRGC2","IL2RB","KLRB1","NCR1","NKG7","NCAM1","XCL2","XCL1","CD160","KLRC1"),
Mac=c("VCAN","S100A8","MNDA","LYZ","FCN1","CXCL8","VCAN","VCAM1","TTYH3","TIMD4","SLC40A1","RAB31","MARCO","HMOX1","C1QC"),
Chol=c("PROM1","SOX9","KRT7","KRT19","CFTR","EPCAM","CLDN4","CLDN7","ANXA4","TACSTD2"),
Stel=c("ACTA2","COL1A1","RBP1","TAGLN","ADAMTSL2","GEM","LOXL1","LUM"),
Endo=c("PECAM1","TAGLN","VWF","FLT1","MMRN1","RSPO3","LYPD2","LTC4S","TSHZ2","IL1R1")
)

So in short, I need to solve this issue and any help will be appreciated.

Thank you