I am trying to analyze two different RNA Seq experimental data ( Two different experiments, (different runs), same platform). I would like to normalize the data from both the experiments together, to gain some insights on cell type specific expression profile (for a preliminary evaluation).
In such a case, can some one tell me how can I do the normalization (any established methods?). Any directions on what are the possible challenges and any directions towards this approach would be of great help.
Thanks in advance!