%0 Journal Article
%T Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data
%A Kerby Shedden
%A Wei Chen
%A Rork Kuick
%A Debashis Ghosh
%A James Macdonald
%A Kathleen R Cho
%A Thomas J Giordano
%A Stephen B Gruber
%A Eric R Fearon
%A Jeremy MG Taylor
%A Samir Hanash
%J BMC Bioinformatics
%D 2005
%I BioMed Central
%R 10.1186/1471-2105-6-26
%X In the two data sets considered here, up to seven-fold variation across the processing methods was found in the number of genes detected at a given false discovery rate (FDR). The best performing methods called up to 90% of the same genes differentially expressed, had less variable test statistics under randomization, and had a greater number of large test statistics in the experimental data. Poor performance of one method was directly tied to a tendency to produce highly variable test statistic values under randomization. Based on an overall measure of performance, two of the seven methods (Dchip and a trimmed mean approach) are superior in the two data sets considered here. Two other methods (MAS5 and GCRMA-EB) are inferior, while results for the other three methods are mixed.Choice of processing method has a major impact on differential expression analysis of microarray data. Previously reported performance analyses using tightly controlled calibration data sets are not highly consistent with results reported here using data from human tissue samples. Performance of array processing methods in disease profiling and other realistic biological studies should be given greater consideration when comparing Affymetrix processing methods.Affymetrix microarrays are high throughput assays for measuring the expression levels of thousands of gene transcripts simultaneously. This type of microarray measures the expression of each transcript multiple times through a set of "probe pairs". Since the advent of the Affymetrix microarray, numerous methods have been proposed for producing numerical expression summaries for each transcript based on the probe pair data. Several systematic studies have appeared comparing a number of methods on a common basis (e.g. [1-5]). These studies rely heavily on calibration data sets derived from spike-in, dilution series, and mixture experiments for comparing methods. Our goal here was to carry out a comparative study of Affymetrix array proces
%U http://www.biomedcentral.com/1471-2105/6/26