PANP is a method which offers an improved presence/absence detection call for gene expression profiling of HG-U133 and HG-U133Plus2 Affymetrix chips.
This method has been accepted into the Bioconductor project, and is expected to be included with the release of Bioconductor 1.8.
The panp package is available at "panp" on the contribution/development package website at Bioconductor.
Paper on PANP is available as a [Preprint PDF], accepted to BIBE07 (2007).
PANP supplemental info (MS Word)
PANP vs. Half-price analysis by Wu and Irizarry (MS Word)