Due to an array reagent issue on the QIMR run arrays which affected ‘top’ strand SNPs more than ‘bottom’ strand SNPs, the degree of normalization (amount by which red beadscores were rescaled) on the arrays varied by strand. Whilst results are broadly similar on both strands, the array reagent issue meant that the results from “bottom” strand SNPs showed lower levels of pooling error. We hence focused on the set of “bottom” strand SNPs in QIMR run arrays. In the deCODE run arrays (where there were no array reagent issues), both strands performed similarly.
