I am doing an expression analysis of rna seq dataset I have some doubts to be clarified
can we do an analysis by choosing controls and test from two different datasets?
One of the rna seq dataset is human(test is taken) and the other (control )is rat .is it possible to do differential expression this way?
In total I have three datasets for expression analysis. I did PCA before which I removed batch effects in deseq2.is it enough to remove the batch effect?..or should I do anything more ?
please do help