Using RNA sample titrations to assess microarray platform performance and normalization techniques

被引：123

作者：

Shippy, Richard

Fulmer-Smentek, Stephanie

Jensen, Roderick V.

Jones, Wendell D.

Wolber, Paul K.

Johnson, Charles D.

Pine, P. Scott

Boysen, Cecilie

Guo, Xu

Chudin, Eugene

Sun, Yongming Andrew

Willey, James C.

Thierry-Mieg, Jean

Thierry-Mieg, Danielle

Setterquist, Robert A.

Wilson, Mike

Lucas, Anne Bergstrom

Novoradovskaya, Natalia

Papallo, Adam

Turpaz, Yaron

Baker, Shawn C.

Warrington, Janet A.

Shi, Leming

Herman, Damir

机构：

[1] GE Healthcare, Tempe, AZ 85284 USA

[2] Agilent Technol, Santa Clara, CA 95051 USA

[3] Univ Massachusetts, Boston, MA 02125 USA

[4] Express Anal Inc, Durham, NC 27713 USA

[5] Asuragen Inc, Austin, TX 78744 USA

[6] US FDA, Ctr Drug Evaluat & Res, Silver Spring, MD 20993 USA

[7] ViaLogy, Altadena, CA 91001 USA

[8] Affymetrix Inc, Santa Clara, CA 95051 USA

[9] Illumina Inc, San Diego, CA 92121 USA

[10] Appl Biosyst Inc, Foster City, CA 94404 USA

[11] Univ Toledo, Toledo, OH 43606 USA

[12] Natl Ctr Biotechnol Informat, Bethesda, MD 20894 USA

[13] Appl Biosyst Inc, Austin, TX 78744 USA

[14] Stratagene, La Jolla, CA 92037 USA

[15] US FDA, Natl Ctr Toxicol Res, Jefferson, AR 72079 USA

来源：

NATURE BIOTECHNOLOGY | 2006年 / 24卷 / 09期

关键词：

D O I：

10.1038/nbt1241

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页码：1123 / 1131

页数：9

共 31 条

[21] Expression profiling with oligonucleotide arrays: Technologies and applications for neurobiology [J].

Sendera, TJ ;

Dorris, D ;

Ramakrishnan, R ;

Nguyen, A ;

Trakas, D ;

Mazumder, A .

NEUROCHEMICAL RESEARCH, 2002, 27 (10) :1005-1026

[22] An interactive power analysis tool for microarray hypothesis testing and generation [J].

Seo, J ;

Gordish-Dressman, H ;

Hoffman, EP .

BIOINFORMATICS, 2006, 22 (07) :808-814

[23] The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements [J].

Shi, Leming ;

Reid, Laura H. ;

Jones, Wendell D. ;

Shippy, Richard ;

Warrington, Janet A. ;

Baker, Shawn C. ;

Collins, Patrick J. ;

de Longueville, Francoise ;

Kawasaki, Ernest S. ;

Lee, Kathleen Y. ;

Luo, Yuling ;

Sun, Yongming Andrew ;

Willey, James C. ;

Setterquist, Robert A. ;

Fischer, Gavin M. ;

Tong, Weida ;

Dragan, Yvonne P. ;

Dix, David J. ;

Frueh, Felix W. ;

Goodsaid, Federico M. ;

Herman, Damir ;

Jensen, Roderick V. ;

Johnson, Charles D. ;

Lobenhofer, Edward K. ;

Puri, Raj K. ;

Scherf, Uwe ;

Thierry-Mieg, Jean ;

Wang, Charles ;

Wilson, Mike ;

Wolber, Paul K. ;

Zhang, Lu ;

Amur, Shashi ;

Bao, Wenjun ;

Barbacioru, Catalin C. ;

Lucas, Anne Bergstrom ;

Bertholet, Vincent ;

Boysen, Cecilie ;

Bromley, Bud ;

Brown, Donna ;

Brunner, Alan ;

Canales, Roger ;

Cao, Xiaoxi Megan ;

Cebula, Thomas A. ;

Chen, James J. ;

Cheng, Jing ;

Chu, Tzu-Ming ;

Chudin, Eugene ;

Corson, John ;

Corton, J. Christopher ;

Croner, Lisa J. .

NATURE BIOTECHNOLOGY, 2006, 24 (09) :1151-1161

[24] Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential [J].

Shi, LM ;

Tong, WD ;

Fang, H ;

Scherf, U ;

Han, J ;

Puri, RK ;

Frueh, FW ;

Goodsaid, FM ;

Guo, L ;

Su, ZQ ;

Han, T ;

Fuscoe, JC ;

Xu, ZA ;

Patterson, TA ;

Hong, HX ;

Xie, Q ;

Perkins, RG ;

Chen, JJ ;

Casciano, DA .

BMC BIOINFORMATICS, 2005, 6 (Suppl 2)

[25] Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations [J].

Shippy, R ;

Sendera, TJ ;

Lockner, R ;

Palaniappan, C ;

Kaysser-Kranich, T ;

Watts, G ;

Alsobrook, J .

BMC GENOMICS, 2004, 5 (1)

[26] Use of a mixed tissue RNA design for performance assessments on multiple microarray formats [J].

Thompson, KL ;

Rosenzweig, BA ;

Pine, PS ;

Retief, J ;

Turpaz, Y ;

Afshari, CA ;

Hamadeh, HK ;

Damore, MA ;

Boedigheimer, M ;

Blomme, E ;

Ciurlionis, R ;

Waring, JF ;

Fuscoe, JC ;

Paules, R ;

Tucker, CJ ;

Fare, T ;

Coffey, EM ;

He, Y ;

Collins, PJ ;

Jarnagin, K ;

Fujimoto, S ;

Ganter, B ;

Kiser, G ;

Kaysser-Kranich, T ;

Sina, J ;

Sistare, FD .

NUCLEIC ACIDS RESEARCH, 2005, 33 (22) :e187

[27] A simple method for assessing sample sizes in microarray experiments [J].

Tibshirani, R .

BMC BIOINFORMATICS, 2006, 7 (1)

[28] Evaluation of external RNA controls for the assessment of microarray performance [J].

Tong, Weida ;

Lucas, Anne Bergstrom ;

Shippy, Richard ;

Fan, Xiaohui ;

Fang, Hong ;

Hong, Huixiao ;

Orr, Michael S. ;

Chu, Tzu-Ming ;

Guo, Xu ;

Collins, Patrick J. ;

Sun, Yongming Andrew ;

Wang, Sue-Jane ;

Bao, Wenjun ;

Wolfinger, Russell D. ;

Shchegrova, Svetlana ;

Guo, Lei ;

Warrington, Janet A. ;

Shi, Leming .

NATURE BIOTECHNOLOGY, 2006, 24 (09) :1132-1139

[29] Stochastic models inspired by hybridization theory for short oligonucleotide arrays [J].

Wu, ZJ ;

Irizarry, RA .

JOURNAL OF COMPUTATIONAL BIOLOGY, 2005, 12 (06) :882-893

[30] A model-based background adjustment for oligonucleotide expression arrays [J].

Wu, ZJ ;

Irizarry, RA ;

Gentleman, R ;

Martinez-Murillo, F ;

Spencer, F .

JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, 2004, 99 (468) :909-917

← 1 2 3 4 →