I have a general question relating to data quality control procedures for genome wide association studies. I have two different microarray chips from two different sets of genotyped subjects.
The following data quality cutoffs have been applied to the first chip: minor allele frequency (MAF) > 0.03, individual call rate > 0.98 and genotype call rate > 0.98 and Hardy-Weinberg equilibrium (HWE) P > 0.001.
Sorry to be simplistic but my question is would you advise applying the same data quality measures to the second chip, and if not does how would any biological interpretation from later data analyses be effected by the different data quality procedures ? Thanks!