Feature-level exploration of a published Affymetrix GeneChip control dataset.docVIP

Correspondence Feature-level exploration of a published Affymetrix GeneChip control dataset Rafael A Irizarry*, Leslie M Cope? and Zhijin Wu? A comment on Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset by SE Choe, M Boutros, AM Michelson, GM Church and MS Halfon. Genome Biology 2005, 6:R16. Addresses: *Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205- 2179, USA. ?Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 550 N. Broadway, Suite 1131 Baltimore, MD 21205, USA. ?Center for Statistical Sciences, Department of Community Health, Brown University, 167 Angell Street, Providence, RI 02912, USA. Correspondence: Rafael A Irizarry. Email: rafa@ Published: 1 September 2005 Genome Biology 2006, 7:404 (doi:10.1186/gb-2006-7-8-404) The electronic version of this article is the complete one and can be found online at /2006/7/8/404 ? 2006 BioMed Central Ltd In a recent Genome Biology article, Choe et al. [1] describe a spike-in experiment that they use to compare expression measures for Affymetrix GeneChip technology. In this work, two sets of triplicates were created to repre- sent control (C) and experimental (S) produced by [1] which we believe Correspondence). Figure 1b demon- explain these inconsistencies. These strates that in a typical experiment [6], can be divided into characteristics features related to differentially induced by the experimental design and an artifact. expressed genes show intensities with a similar range as the rest of the genes - in particular, that less than 10% of genes, including the differentially samples. We describe here some prop- Experimental design expressed genes, are above intensities of 10. Figure ADF5-3 in the Additional data files for [1] shows that less than 20% of