AffyGCQC: a web-based interface to detect outlying genechips with extreme studentized deviate tests.

Affymetrix GeneChip oligonucleotide arrays are dedicated to analyzing gene expression differences across distinct experimental conditions. Data production for such arrays is an elaborate process with many potential sources of variability unrelated to biologically relevant gene expression variations. Therefore, rigorous data quality assessment is fundamental throughout the process for downstream biologically meaningful analyses. We have developed a program named AffyGCQC, which is the acronym for a bioinformatics tool designed to perform Affymetrix GeneChip Quality Control. This program implements a graphical representation of QC metrics recommended by Affymetrix for GeneChip oligonucleotide array technology. Most importantly, it performs extreme studentized deviate statistical tests for the set of arrays being compared in a given experiment, thus providing an objective measure for outlier detection. AffyGCQC has been designed as an easy-to-use Web-based interface (online supplementary information: http://www.transcriptome.ens.fr/AffyGCQC/; contact: affygcqc@biologie.ens.fr).