MOTIVATION In the Affymetrix GeneChip system, preprocessing occurs before one obtains expression level measurements. Because the number of competing preprocessing methods was large and growing we developed a benchmark to help users identify the best method for their application. A webtool was made available for developers to benchmark their procedures. At the time of writing over 50 methods had...

The approximately 25,000 genes in mammalian genomes can be transcribed at different levels. Measurements of gene expression for ten thousands of genes in parallel give the most comprehensive picture of steady-state levels of transcripts and is used in basic and applied research. Microarrays are the most frequently used technology for genome-wide expression profiling; from the various available ...

DNA microarrays can be classified into oligonucleotides (Affymetrix) or long cDNAs (IncyteGenomics) based on the arrayed probes. Unfortunately, data are lacking on the comparison of these two popular global screening array systems. The present study was designed to assess the reliability of datasets generated by the two platforms from the same samples. We have already established a model for up...

In this paper we develop a new method for genotyping Affymetrix single nucleotide polymorphism (SNP) array. The method is based on (i) using multiple arrays at the same time to determine the genotypes and (ii) a model that relates intensities of individual SNPs to each other. The latter point allows us to annotate SNPs that have poor performance, either because of poor experimental conditions o...

Large-scale microarray expression profiling studies have helped us to understand basic biological processes and to classify and predict the prognosis of cancers; they have also accelerated the identification of new drug targets. Affymetrix GeneChip probe arrays are high-density oligonucleotide microarrays that are available for many prokaryotic and eukaryotic species. Affymetrix human and mouse...

Transcript profiling is crucial to study biological systems, and various platforms have been implemented to survey mRNAs at the genome scale. We have assessed the performance of the CATMA microarray designed for Arabidopsis (Arabidopsis thaliana) transcriptome analysis and compared it with the Agilent and Affymetrix commercial platforms. The CATMA array consists of gene-specific sequence tags o...