I've been trying to create a Seurat object:
nuc.seurat <- CreateSeuratObject(counts = as.matrix(UMIs), project = i, min.cells = 3, min.features = 200)
however I keep on getting the following error:
Error in validObject(.Object) :
invalid class “LogMap” object: Rownames must be supplied
The weird thing is, just a day ago it worked completely fine with the exact same pipline. UMIs in this case is a count dataframe, and it has rownames (despite what the error is suggesting):
Sample1 Sample2 Sample3 Sample4
A1BG 21 0 6 1
A1BG-AS1 2 0 0 0
A1CF 9 3 8 2
A2M 17 0 4 0
A2M-AS1 0 0 0 0
(UMIs is a lot larger this is just a subset)
I do not have a lot of experience in R or using Seurat so any input would help! Thank you!
I have tried removing some pf the input args of CreateSeuratObject and that did work:
nuc.seurat <- CreateSeuratObject(counts = as.matrix(UMIs), project = i, min.cells = 3)
However, filtering by min.features at this step reduces object size and eliminates other error down the line (NA data and so on). So it's not a good enough solution.