I am trying to use mnnCorrect to identify shared cell population between two batches from different conditions - WT and KO.
classic.out <- batchelor::mnnCorrect(sce1, sce2, subset.row=chosen.hvgs , correct.all = TRUE)
Using HVGs as input to mnnCorrect function, I get:
> classic.out class: SingleCellExperiment dim: 9608 2542 metadata(1): merge.info assays(1): corrected rownames(9608): ENSMUSG00000000056.7 ENSMUSG00000000078.7 ... NA NA Error in `rownames<-`(`*tmp*`, value = c("ENSMUSG00000000056.7", "ENSMUSG00000000078.7", : missing values not allowed in rownames
There are no NAs in the individual single cell objects. Can you please help with the error.