I have multiple datasets from different platforms (Illumina and Affymetrix) and I have already performed a differential expression analysis for these datasets individually. I have used RMA and rsn normalization methods for Affymetrix and Illumina respectively. Now, I plan to perform a meta-analysis for these datasets. But, I am really not sure about the normalization method to be used before combining these datasets in the analysis. Following are my queries regarding the same:
- Is it necessary to use the same normalization method for all the datasets before combining them for further analysis?
- If yes, which method is recommended in this case? (considering the datasets are from two different platforms)
- If no, how can it affect the meta-analysis analysis? (wherein I plan to quantile normalise the combined file before going for differential expression)
I would really appreciate any response to my queries. It would be a great help if could direct me to the appropriate literature. Also, I would appreciate it, if you all can make me aware of the available packages for meta-analysis if any.