I found this interesting Single RNA-seq data set in GEO, but I am not sure how to analyze it oppropritly.

They have deposited transcriptomic profiles of human and mouse pancreatic islets (pancreatic cells: Beta cells, Delta, etc). The problem I see is that the different panacratic cell types are not in equal numbers; for example, the total number of Beta cells that have been isolated is more than Delta cells.

What I am interested to do is to compare the expression of two panacriatic cell types (Beta v.s. Delta cells) using scatter plot.

Question: Given unequal number of isolated panacriatic cells, what would be an appropriate way to compare the expression profiles? Should I just ignore the extra ones?

Any idea how to approch this problem?

Thanks,