Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements

Background: Affymetrix GeneChip microarrays are popular platforms for expression profiling in two types of studies: detection of differential expression computed by p-values of t-test and estimation of fold change between analyzed groups. There are many different preprocessing algorithms for summarizing Affymetrix data. The main goal of these methods is to remove effects of non-specific hybridization, and to optimally combine information from multiple probes annotated to the same transcript. The methods are benchmarked by comparison with reference methods, such as quantitative reverse-transcription PCR (qRT-PCR). Results: We present a comprehensive analysis of agreement between Affymetrix GeneChip and qRT-PCR results. We analyzed the influence of filtering by fraction Present calls introduced by J.N. McClintick and H.J. Edenberg (2006) and 2 mapping procedures: updated probe sets definitions proposed by Dai et al. (2005) and our "naive mapping" method. Because of evolution o...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Jakub Mieczkowski, Magdalena E. Tyburczy, Michal Dabrowski, Piotr Pokarowski
• Keywords: Affymetrix, BMCBI 2010, Fold Change, Quantitative Reverse-transcription Pcr