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- Title
Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays.
- Authors
Seo, Jinwook; Bakay, Marina; Chen, Yi-Wen; Hilmer, Sara; Shneiderman, Ben; Hoffman, Eric P
- Abstract
The most commonly utilized microarrays for mRNA profiling (Affymetrix) include 'probe sets' of a series of perfect match and mismatch probes (typically 22 oligonucleotides per probe set). There are an increasing number of reported 'probe set algorithms' that differ in their interpretation of a probe set to derive a single normalized 'signal' representative of expression of each mRNA. These algorithms are known to differ in accuracy and sensitivity, and optimization has been done using a small set of standardized control microarray data. We hypothesized that different mRNA profiling projects have varying sources and degrees of confounding noise, and that these should alter the choice of a specific probe set algorithm. Also, we hypothesized that use of the Microarray Suite (MAS) 5.0 probe set detection p-value as a weighting function would improve the performance of all probe set algorithms.
- Publication
Bioinformatics (Oxford, England), 2004, Vol 20, Issue 16, p2534
- ISSN
1367-4803
- Publication type
Journal Article
- DOI
10.1093/bioinformatics/bth280