A distribution free summarization method for Affymetrix GeneChip® arrays | Zendy

Zhongxue Chen | Zendy; Monnie McGee | Zendy; Qingzhong Liu | Zendy; Richard H. Scheuermann | Zendy

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A distribution free summarization method for Affymetrix GeneChip® arrays

Author(s) -

Zhongxue Chen,

Monnie McGee,

Qingzhong Liu,

Richard H. Scheuermann

Publication year - 2006

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btl609

Subject(s) - automatic summarization , computer science , false positive paradox , sensitivity (control systems) , data mining , artificial intelligence , electronic engineering , engineering

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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