Removing batch effects from purified plasma cell gene expression microarrays with modified ComBat.

ABSTRACT:

Background

Gene expression profiling (GEP) via microarray analysis is a widely used tool for assessing risk and other patient diagnostics in clinical settings. However, non-biological factors such as systematic changes in sample preparation, differences in scanners, and other potential batch effects are often unavoidable in long-term studies and meta-analysis. In order to reduce the impact of batch effects on microarray data, Johnson, Rabinovic, and Li developed ComBat for use when combining batches of gene expression microarray data. We propose a modification to ComBat that centers data to the location and scale of a pre-determined, 'gold-standard' batch. This modified ComBat (M-Combat) is designed specifically in the context of meta-analysis and batch effect adjustment for use wi

SUBMITTER: Stein CK 

PROVIDER: S-EPMC4355992 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature