single population RNAseq microglia contamination

Question

[deprisco.nicola]

Hello, I'm Nicola from Italy. I've a question about one of mine RNA-seq dataset. I did single population of a subclass of cells in the retina, after sorting, doing differential expression analysis between this and another class of cells from retina. In all the biological replicates, for some reason, i found also microglial markers that contaminate my differential expression analysis. For this reason i found in the GO description class related to immunity. I need to clean my dataset!

Someone have some advice to solve this problem??

thanks in advance

Nicola