title: Evaluation of external RNA controls for the assessment of microarray performance.
abstract: External RNA controls (ERCs), although important for microarray assay performance assessment, have yet to be fully implemented in the research community. As part of the MicroArray Quality Control (MAQC) study, two types of ERCs were implemented and evaluated; one was added to the total RNA in the samples before amplification and labeling; the other was added to the copyRNAs (cRNAs) before hybridization. ERC concentration-response curves were used across multiple commercial microarray platforms to identify problematic assays and potential sources of variation in the analytical process. In addition, the behavior of different ERC types was investigated, resulting in several important observations, such as the sample-dependent attributes of performance and the potential of using these control RNAs in a combinatorial fashion. This multiplatform investigation of the behavior and utility of ERCs provides a basis for articulating specific recommendations for their future use in evaluating assay performance across multiple platforms.
authors.affiliation: National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., Jefferson, Arkansas 72079, USA. weida.tong@fda.hhs.gov
authors.forename: Weida
authors.initials: W
authors.lastname: Tong
authors.forename: Anne Bergstrom
authors.initials: AB
authors.lastname: Lucas
authors.forename: Richard
authors.initials: R
authors.lastname: Shippy
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Fan
authors.forename: Hong
authors.initials: H
authors.lastname: Fang
authors.forename: Huixiao
authors.initials: H
authors.lastname: Hong
authors.forename: Michael S
authors.initials: MS
authors.lastname: Orr
authors.forename: Tzu-Ming
authors.initials: TM
authors.lastname: Chu
authors.forename: Xu
authors.initials: X
authors.lastname: Guo
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Collins
authors.forename: Yongming Andrew
authors.initials: YA
authors.lastname: Sun
authors.forename: Sue-Jane
authors.initials: SJ
authors.lastname: Wang
authors.forename: Wenjun
authors.initials: W
authors.lastname: Bao
authors.forename: Russell D
authors.initials: RD
authors.lastname: Wolfinger
authors.forename: Svetlana
authors.initials: S
authors.lastname: Shchegrova
authors.forename: Lei
authors.initials: L
authors.lastname: Guo
authors.forename: Janet A
authors.initials: JA
authors.lastname: Warrington
authors.forename: Leming
authors.initials: L
authors.lastname: Shi
mesh_terms: D000465:Algorithms; D019544:Equipment Failure Analysis / Q000379:methods*; D020869:Gene Expression Profiling / Q000295:instrumentation* / Q000592:standards*; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000592:standards*; D012313:RNA / Q000032:analysis* / Q000235:genetics* / Q000592:standards; D012016:Reference Values; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D014481:United States
chemical_list: D012313:RNA