title: Summaries of Affymetrix GeneChip probe level data.
abstract: High density oligonucleotide array technology is widely used in many areas of biomedical research for quantitative and highly parallel measurements of gene expression. Affymetrix GeneChip arrays are the most popular. In this technology each gene is typically represented by a set of 11-20 pairs of probes. In order to obtain expression measures it is necessary to summarize the probe level data. Using two extensive spike-in studies and a dilution study, we developed a set of tools for assessing the effectiveness of expression measures. We found that the performance of the current version of the default expression measure provided by Affymetrix Microarray Suite can be significantly improved by the use of probe level summaries derived from empirically motivated statistical models. In particular, improvements in the ability to detect differentially expressed genes are demonstrated.
authors.affiliation: Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA. rafa@jhu.edu
authors.forename: Rafael A
authors.initials: RA
authors.lastname: Irizarry
authors.forename: Benjamin M
authors.initials: BM
authors.lastname: Bolstad
authors.forename: Francois
authors.initials: F
authors.lastname: Collin
authors.forename: Leslie M
authors.initials: LM
authors.lastname: Cope
authors.forename: Bridget
authors.initials: B
authors.lastname: Hobbs
authors.forename: Terence P
authors.initials: TP
authors.lastname: Speed
mesh_terms: D002490:Central Nervous System / Q000378:metabolism; D015342:DNA Probes / Q000235:genetics* / Q000592:standards; D020869:Gene Expression Profiling; D006801:Humans; D008099:Liver / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D012984:Software
chemical_list: D015342:DNA Probes; D012333:RNA, Messenger