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?
I do not see how this makes sense. The number of differential genes just by the species different (even if you manage to normalize the homologs) will overwhelm this, regardless of the treatment.
Look, there is no magic way around a proper study design. If you want to compare treatment vs control in a proper and unbiased manner then get a model (cell lines, mice, flies, rats), expose it to the treatment and control, and then assay the specimen.