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2008

Empirical Bayes models for multiple probe type microarrays at the probe level

11 years 5 months ago
Empirical Bayes models for multiple probe type microarrays at the probe level
Background: When analyzing microarray data a primary objective is often to find differentially expressed genes. With empirical Bayes and penalized t-tests the sample variances are adjusted towards a global estimate, producing more stable results compared to ordinary t-tests. However, for Affymetrix type data a clear dependency between variability and intensity-level generally exists, even for logged intensities, most clearly for data at the probe level but also for probe-set summarizes such as the MAS5 expression index. As a consequence, adjustment towards a global estimate results in an intensity-level dependent false positive rate. Results: We propose two new methods for finding differentially expressed genes, Probe level Locally moderated Weighted median-t (PLW) and Locally Moderated Weighted-t (LMW). Both methods use an empirical Bayes model taking the dependency between variability and intensitylevel into account. A global covariance matrix is also used allowing for differing var...
Magnus Åstrand, Petter Mostad, Mats Rudemo
Added 08 Dec 2010
Updated 08 Dec 2010
Type Journal
Year 2008
Where BMCBI
Authors Magnus Åstrand, Petter Mostad, Mats Rudemo
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