The effect of tumour expression and genotypes on apparent matching quality.

<p>For 127 quartets of matched tumour-and-normal genotype-and-expression arrays we illustrate the relative quality of the matches between the four different expression-genotype combinations. The 127 genotype array pairs are all clearly well-matched (not shown). Our approach is to identify the quality of a genotype array’s match to an expression array, and all results given are reflective of this direction of comparison. For the sets of tumour and normal expression arrays, indicated in the arrows are the number of expression arrays for which the two genotyping arrays are equally good matches (have the same genotype calls), the number for which the tumour genotyping array for that sample has a better score than the normal genotyping array, and vice versa. Additionally, in the corner panels, the BADGER ranks for the matches amongst the entire data set to which we have access are presented.