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

ABSTRACT:

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

SUBMITTER: Astrand M 

PROVIDER: S-EPMC2358895 | biostudies-literature | 2008 Mar

REPOSITORIES: biostudies-literature