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EDIT:
I also get this when I try to use many levels:
Regressing out batch
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) :
contrasts can be applied only to factors with 2 or more levels
> ce
An object of class Seurat
13336 features across 50032 samples within 1 assay
Active assay: RNA (13336 features, 0 variable features)
12 layers present: counts.nf1, counts.om1, counts.of2, ...
> ce <- SCTransform(cv, vars.to.regress='Batch', verbose=FALSE)
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) :
contrasts can be applied only to factors with 2 or more levels
> str(ce$Batch)
Factor w/ 2 levels "A","B": 1 1 1 1 1 1 1 1 1 1 ...
- attr(*, "names")= chr [1:50032] "om1_TACTGCCCAACCACGC-1 ...
> table(ce$Batch)
A B
40787 9245
When running:
soup_obj <- SCTransform(soup_obj, vars.to.regress="Sex")
I get the error:
But my variable "Sex" is a factor with two levels:
Seurat_5.0.3
EDIT:
I also get this when I try to use many levels:
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