I am trying to perform a meta-analysis using microarray data of 6 datasets with different platforms (Illumina HumanHT-12 V4.0 expression beadchip, Affymetrix Human Exon 1.0 ST Array, Affymetrix Human Gene 1.0 ST Array).
My question is about the first step of meta-analysis which is data normalization (before merging the data and remove the batch effect), may I normalize all of the dataset simultaneous (for example using the LIMMA package)? Or must be normalized them separately? Which way is correct and the best way?
Thank you in advance.