Dear SMLG Members,
I'm working on a mayo clinic RNA-Seq cohort where datasets I've compiled are derived from three separate labs. In the attachment you can find the raw data from each of these three separate labs, annotated by ensemble ID. If you can help me with the normalization of this data from across three datasets I would be greatly appreciative. The Dr. Taner dataset attached represents Cerebellum data from 200 Cerebral Amyloid Angiopathy Cases derived from this synapse repository: https://www.synapse.org/#!Synapse:syn10930230. The Dr. Bu dataset attached represents Temporal Cortex data from 75 Cerebral Amyloid Angiopathy Cases. Lastly, my Control dataset attached represents data from the Mayo-Clinic AD Cohort and can be found in this synapse repository: https://www.synapse.org/#!Synapse:syn5550404. I would like to see what would be best to normalize this data. I've normalized the data according to the Trim Mean Normalization method across all three separate datasets. I'm interested to see any other normalization methods that can help me compare cases and controls between these three studies. Thank you.
CP