title: Using RNA sample titrations to assess microarray platform performance and normalization techniques.
abstract: We have assessed the utility of RNA titration samples for evaluating microarray platform performance and the impact of different normalization methods on the results obtained. As part of the MicroArray Quality Control project, we investigated the performance of five commercial microarray platforms using two independent RNA samples and two titration mixtures of these samples. Focusing on 12,091 genes common across all platforms, we determined the ability of each platform to detect the correct titration response across the samples. Global deviations from the response predicted by the titration ratios were observed. These differences could be explained by variations in relative amounts of messenger RNA as a fraction of total RNA between the two independent samples. Overall, both the qualitative and quantitative correspondence across platforms was high. In summary, titration samples may be regarded as a valuable tool, not only for assessing microarray platform performance and different analysis methods, but also for determining some underlying biological features of the samples.
authors.affiliation: GE Healthcare, 7700 S. River Pkwy., Suite #2603, Tempe, Arizona 85284, USA. richard.shippy@ge.com
authors.forename: Richard
authors.initials: R
authors.lastname: Shippy
authors.forename: Stephanie
authors.initials: S
authors.lastname: Fulmer-Smentek
authors.forename: Roderick V
authors.initials: RV
authors.lastname: Jensen
authors.forename: Wendell D
authors.initials: WD
authors.lastname: Jones
authors.forename: Paul K
authors.initials: PK
authors.lastname: Wolber
authors.forename: Charles D
authors.initials: CD
authors.lastname: Johnson
authors.forename: P Scott
authors.initials: PS
authors.lastname: Pine
authors.forename: Cecilie
authors.initials: C
authors.lastname: Boysen
authors.forename: Xu
authors.initials: X
authors.lastname: Guo
authors.forename: Eugene
authors.initials: E
authors.lastname: Chudin
authors.forename: Yongming Andrew
authors.initials: YA
authors.lastname: Sun
authors.forename: James C
authors.initials: JC
authors.lastname: Willey
authors.forename: Jean
authors.initials: J
authors.lastname: Thierry-Mieg
authors.forename: Danielle
authors.initials: D
authors.lastname: Thierry-Mieg
authors.forename: Robert A
authors.initials: RA
authors.lastname: Setterquist
authors.forename: Mike
authors.initials: M
authors.lastname: Wilson
authors.forename: Anne Bergstrom
authors.initials: AB
authors.lastname: Lucas
authors.forename: Natalia
authors.initials: N
authors.lastname: Novoradovskaya
authors.forename: Adam
authors.initials: A
authors.lastname: Papallo
authors.forename: Yaron
authors.initials: Y
authors.lastname: Turpaz
authors.forename: Shawn C
authors.initials: SC
authors.lastname: Baker
authors.forename: Janet A
authors.initials: JA
authors.lastname: Warrington
authors.forename: Leming
authors.initials: L
authors.lastname: Shi
authors.forename: Damir
authors.initials: D
authors.lastname: Herman
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*; D012016:Reference Values; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D014481:United States
chemical_list: D012313:RNA