Chen Z, McGee M, Liu Q, Scheuermann RH
A Distribution Free Summarization Method for Affymetrix GeneChip Arrays.
Bioinformatics (Oxford, England). 2007 Feb 01; 23: 321-7.
Affymetrix GeneChip arrays require summarization in order to combine the probe-level intensities into one value representing the expression level of a gene. However, probe intensity measurements are expected to be affected by different levels of non-specific- and cross-hybridization to non-specific transcripts. Here, we present a new summarization technique, the Distribution Free Weighted method (DFW), which uses information about the variability in probe behavior to estimate the extent of non-specific and cross-hybridization for each probe. The contribution of the probe is weighted accordingly during summarization, without making any distributional assumptions for the probe-level data.
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