Hi we performed RNA seq on 8 mammary tumors. I wanted to compare our RNA-seq data to raw RNA-seq data that I found online. I plan to process the raw RNA-seq data through the same pipeline. Is it possible to run EdgeR, Deseq, Limma or any other programs to find differentially expressed genes between the two datasets? My main concern is getting rid of batch effects. The issue is that I don't have any normal mammary samples on my RNA-seq to use as control. There is normal and tumor samples on the RNA seq dataset that I downloaded. Anybody have any suggestions?