Nature Biotechnology
- 24, 1123 - 1131 (2006)
Published online: 8 September 2006; | doi:10.1038/nbt1241
Using RNA sample titrations to assess microarray platform performance and normalization techniquesRichard Shippy1, Stephanie Fulmer-Smentek2, Roderick V Jensen3, Wendell D Jones4, Paul K Wolber2, Charles D Johnson5, P Scott Pine6, Cecilie Boysen7, Xu Guo8, Eugene Chudin9, Yongming Andrew Sun10, James C Willey11, Jean Thierry-Mieg12, Danielle Thierry-Mieg12, Robert A Setterquist13, Mike Wilson5, Anne Bergstrom Lucas2, Natalia Novoradovskaya14, Adam Papallo3, Yaron Turpaz8, Shawn C Baker9, Janet A Warrington8, Leming Shi15 & Damir Herman121
GE Healthcare, 7700 S. River Pkwy., Suite #2603, Tempe, Arizona 85284, USA. 2
Agilent Technologies, Inc., 5301 Stevens Creek Blvd., Santa Clara, California 95051, USA. 3
University of Massachusetts-Boston, 100 Morrissey Blvd., Boston, Massachusetts 02125, USA. 4
Expression Analysis, Inc., 2605 Meridian Pkwy., Durham, North Carolina 27713, USA. 5
Asuragen, Inc., 2150 Woodward, Austin, Texas 78744, USA. 6
Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland 20993, USA. 7
ViaLogy, 2400 Lincoln Ave, Altadena, California 91001, USA. 8
Affymetrix, Inc., 3420 Central Expressway, Santa Clara, California 95051, USA. 9
Illumina, Inc., 9885 Towne Centre Dr., San Diego, California 92121, USA. 10
Applied Biosystems, 850 Lincoln Centre Dr., Foster City, California 94404, USA. 11
University of Toledo, Toledo, Ohio 43606, USA. 12
National Center for Biotechnology Information, Bethesda, Maryland 20894, USA. 13
Applied Biosystems, 2150 Woodward, Austin, Texas 78744, USA. 14
Stratagene, 11011 N. Torrey Pines Rd., La Jolla, California 92037, USA. 15
National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., Jefferson, Arizona 72079, USA.
Correspondence should be addressed to Richard Shippy richard.shippy@ge.com 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.
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