Preprocessing of gene expression data by optimally robust estimators

Background: The preprocessing of gene expression data obtained from several platforms routinely includes the aggregation of multiple raw signal intensities to one expression value. Examples are the computation of a single expression measure based on the perfect match (PM) and mismatch (MM) probes for the Affymetrix technology, the summarization of bead level values to bead summary values for the Illumina technology or the aggregation of replicated measurements in the case of other technologies including real-time quantitative polymerase chain reaction (RT-qPCR) platforms. The summarization of technical replicates is also performed in other "-omics" disciplines like proteomics or metabolomics. Preprocessing methods like MAS 5.0, Illumina's default summarization method, RMA, or VSN show that the use of robust estimators is widely accepted in gene expression analysis. However, the selection of robust methods seems to be mainly driven by their high breakdown point and not b...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Matthias Kohl, Hans-Peter Deigner
• Keywords: Affymetrix, BMCBI 2010, Business, Multiple Raw Signal, Raw Signal Intensities