I have two datasets corresponding to two conditions, each of which has been derived by a different sequencing method (RNA-Seq and 3SEQ). Each dataset contains multiple individuals, but no individual appears in both datasets.
Given that each of these sequencing methods introduces different biases (e.g., into the number of counts relative to the length of a gene), is there any way to do a differential expression analysis? Can one 'translate' RNA-Seq data into something with 3SEQ biases, or vice versa? Can one account for the biases statistically?
Thank you for any insights you can provide.