I am working on GWAS. Currently, I have the genotyping datasets based on two kinds of Axiom arrays: Axiom™ Biobank Genotyping Array (https://www.thermofisher.com/order/catalog/product/902186?SID=srch-srp-902186#/902186?SID=srch-srp-902186) and Axiom™ Transplant Genotyping Array (https://www.thermofisher.com/order/catalog/product/902865?SID=srch-srp-902865#/902865?SID=srch-srp-902865). I want to merge the samples detected by two platforms. However, I am not clear whether two array platforms can be merged for further GWAS analysis.
I obtained their Annotation Files from http://www.affymetrix.com/support/technical/byproduct.affx?cat=arrays. The number of variants included by two platforms are similar but slightly different. Axiom_BioBank1.na35.annot.csv (718232 rows) Axiom_tx_v1.na35.annot.csv (785214 rows)
By the way, the content for each common variant are the same in two annotation files.
My question is whether I can merge two platforms and how?