title: Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project.
abstract: Microarray-based expression profiling experiments typically use either a one-color or a two-color design to measure mRNA abundance. The validity of each approach has been amply demonstrated. Here we provide a simultaneous comparison of results from one- and two-color labeling designs, using two independent RNA samples from the Microarray Quality Control (MAQC) project, tested on each of three different microarray platforms. The data were evaluated in terms of reproducibility, specificity, sensitivity and accuracy to determine if the two approaches provide comparable results. For each of the three microarray platforms tested, the results show good agreement with high correlation coefficients and high concordance of differentially expressed gene lists within each platform. Cumulatively, these comparisons indicate that data quality is essentially equivalent between the one- and two-color approaches and strongly suggest that this variable need not be a primary factor in decisions regarding experimental microarray design.
authors.affiliation: National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Rd., Jefferson, Arkansas 72079, USA. tucker.patterson@fda.hhs.gov
authors.forename: Tucker A
authors.initials: TA
authors.lastname: Patterson
authors.forename: Edward K
authors.initials: EK
authors.lastname: Lobenhofer
authors.forename: Stephanie B
authors.initials: SB
authors.lastname: Fulmer-Smentek
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Collins
authors.forename: Tzu-Ming
authors.initials: TM
authors.lastname: Chu
authors.forename: Wenjun
authors.initials: W
authors.lastname: Bao
authors.forename: Hong
authors.initials: H
authors.lastname: Fang
authors.forename: Ernest S
authors.initials: ES
authors.lastname: Kawasaki
authors.forename: Janet
authors.initials: J
authors.lastname: Hager
authors.forename: Irina R
authors.initials: IR
authors.lastname: Tikhonova
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Walker
authors.forename: Liang
authors.initials: L
authors.lastname: Zhang
authors.forename: Patrick
authors.initials: P
authors.lastname: Hurban
authors.forename: Francoise
authors.initials: F
authors.lastname: de Longueville
authors.forename: James C
authors.initials: JC
authors.lastname: Fuscoe
authors.forename: Weida
authors.initials: W
authors.lastname: Tong
authors.forename: Leming
authors.initials: L
authors.lastname: Shi
authors.forename: Russell D
authors.initials: RD
authors.lastname: Wolfinger
mesh_terms: D004867:Equipment Design; D019544:Equipment Failure Analysis; D020869:Gene Expression Profiling / Q000295:instrumentation* / Q000379:methods; D017404:In Situ Hybridization, Fluorescence / Q000295:instrumentation*; D036641:Microscopy, Fluorescence, Multiphoton / Q000295:instrumentation* / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation*; D011785:Quality Assurance, Health Care / Q000379:methods*; D011786:Quality Control; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D013050:Spectrometry, Fluorescence / Q000295:instrumentation* / Q000379:methods; D014481:United States