The beadscores required normalization/calibration because green beadscores were generally larger than red beadscores. The Illumina 1M v1 arrays had 20 stripes per array, each with ~50000 SNPs. The Illumina 1M v3 arrays had 6 stripes per array, each with ~200000 SNPs. Note that these ‘stripes’ were previously denoted ‘strands’ but this is now changed to avoid confusion with top/bottom strand. Within each stripe, approximately half of the SNPs were from the Illumina ‘top’ strand (A/C and A/G SNPs) and half were from the Illumina ‘bottom’ strand (T/C and T/G SNPs). Normalization was done within stripe by rescaling the red beadscore to make the mean value of the pooling allele frequency (PAF) =0.5 (over all SNPs on that stripe); PAF was computed as the corrected red intensity divided by the total (corrected red plus green) intensity.
