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CSB
2005
IEEE

A Learned Comparative Expression Measure for Affymetrix GeneChip DNA Microarrays

13 years 9 months ago
A Learned Comparative Expression Measure for Affymetrix GeneChip DNA Microarrays
Perhaps the most common question that a microarray study can ask is, “Between two given biological conditions, which genes exhibit changed expression levels?” Existing methods for answering this question either generate a comparative measure based upon a static model, or take an indirect approach, first estimating absolute expression levels and then comparing the estimated levels to one another. We present a method for detecting changes in gene expression between two samples based on data from Affymetrix GeneChips. Using a library of over 200,000 known cases of differential expression, we create a learned comparative expression measure (LCEM) based on classification of probe-level data patterns as changed or unchanged. LCEM uses perfect match probe data only; mismatch probe values did not prove to be useful in this context. LCEM is particularly powerful in the case of small microarry studies, in which a regression-based method such as RMA cannot generalize, and in detecting smal...
Will Sheffler, Eli Upfal, John Sedivy, William Sta
Added 24 Jun 2010
Updated 24 Jun 2010
Type Conference
Year 2005
Where CSB
Authors Will Sheffler, Eli Upfal, John Sedivy, William Stafford Noble
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