I am running the R cellassign algorithm on a set of 9 samples. Each sample consists of cells extracted from lungs. When I look at a UMAP plot and color by sample origin, there is a notable batch effect. So, here's my question..
Can I run the cellassign algorithm on each sample independently for cell typing, or do I have to combine the samples and run the algorithm with correction for batch effect?
I have not been able to find any resources online that take the first approach. The reason I am asking this question is because I am unable to run the algorithm on all the samples combined as I get an out of memory error. Any suggestions/resources are appreciated!