The QA analyses were performed using two software packages, PLINK [Purcell, et al. 2007] and the R statistical package [R Development Core Team 2006]. For analysis in R, the genotypic and quantitative variables (probe intensities, etc.) are stored in netCDF files accessed with the ‘ncdf’ package (see Web Resources). netCDF is a compact storage format that allows rapid access to array-structured datasets. The results presented here were generated in R unless stated otherwise.
