Reference marker normalization

Mullighan et al (2007) normalized their SNP microarray data using a novel reference-marker normalization method. The method is described briefly in the supplementary materials of the article.
We have developed a set of R routines to implement this procedure. This User's Guide may be helpful in getting started.
Here are the SNP annotation data, reference chromosome data, initial signal data, quantile-normalized signals, invariant-set normalized signals, directed reference-normalized signals, and automated reference-normalized signals.
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More questions? Contact Stan Pounds.