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?
Thanks
I got a answer from a technical application scientist of Affymetrix, as shown in following. Wish this can help who have the similar questions.
For all Axiom assays the samples are processed using same core reagent kit with the same process workflow. The only difference is that samples are hybed on different arrays. Axiom array contents are listed in the annotation files with probe selection designed targeted on specific purpose, which usually obvious by assay name. I got internal software support expert reply that different arrays can't be merged. There are a few reasons: QC/control probes are selected differently as well as QC specs. So they should be analyzed separately.