Detecting outlier microarray arrays by correlation and percentage of outliers spots

Cancer Informatics

Volumn 2, Issue , 2006, Pages 351-360

  Yang, Song ^a   Guo, Xiang ^a   Yang, Yaw Ching ^a   Papcunik, Denise ^a   Heckman, Caroline ^a   Hooke, Jeffrey ^b   Shriver, Craig D ^b   Liebman, Michael N ^c   Hu, Hai ^a  

^a WINDBER RESEARCH INSTITUTE   (United States)

^b WALTER REED ARMY MEDICAL CENTER   (United States)

^c NONE

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CORRELATION ANALYSIS; GENE EXPRESSION PROFILING; INFORMATION PROCESSING; METHODOLOGY; MICROARRAY ANALYSIS; QUALITY CONTROL; STATISTICAL ANALYSIS; CONTROLLED STUDY; DNA MICROARRAY; GENE CLUSTER; GENE MAPPING; HUMAN; HYBRIDIZATION; REFERENCE VALUE; RELIABILITY;

EID: 33751355497     PISSN: 11769351     EISSN: 11769351     Source Type: Journal    
DOI: 10.1177/117693510600200017     Document Type: Article

References (16)

1. Allison, D.B., Cui, X., Page, G.P. and Sabripour, M. 2006. Microarray data analysis: from disarray to consolidation and consensus. Nat. Rev. Genet., 7: 55-65.
2. Amaratunga, D. and Cabrera, J. 2004. Resistant rules for outlier identification. Exploration and analysis of DNA microarray and protein array data. John Wiley & Son's, Inc., Hoboken, NJ, US.
3. Burgoon, L.D., Eckel-Passow, J.E., Gennings, C., Boverhof, D.R., Burt, J.W., Fong, C.J. and Zacharewski, T.R. 2005. Protocols for the assurance of microarray data quality and process control. Nucleic Acids Res., 33(19):e172.
4. Chen, Y., Kamat, V., Dougherty, E.R., Bittner, M.L., Meltzer, P.S. and Trent J.M. 2002. Ratio statistics of gene expression levels and applications to microarray data analysis. Bioinformatics, 18(9):1207-15.
5. Golub, T.R., Slonim, D.K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov J.P., Coller, H., Loh, M.L., Downing, J.R., Caligiuri, M.A., Bloomfield, C.D. and Lander, E.S. 1999. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science, 286(5439):531-7.
6. Hautaniemi, S., Edgren, H., Vesanen, P., Wolf, M., Jarvinen, A.K., Yli-Harja, O., Astola, J., Kallioniemi, O. and Monni, O. 2003. A novel strategy for microarray quality control using Bayesian networks. Bioinformatics, 19(16):2031-8.
7. Hu, Y., Hines, L.M., Weng, H., Zuo, D., Rivera, M., Richardson, A. and LaBaer, J. 2003. Analysis of genomic and proteomic data using advanced literature mining. J. Proteome Res., 2(4):405-12.
8. Model, F., Konig, T., Piepenbrock, C. and Adorjan, P. 2002. Statistical process control for large scale microarray experiments. Bioinformatics, 18 Suppl 1:S155-63.
9. Paik, S., Shak, S., Tang, G., Kim, C., Baker, J., Cronin, M., Baehner, F.L., Walker, M.G., Watson, D., Park, T., Hiller, W., Fisher, E.R., Wickerham, D.L., Bryant, J. and Wolmark, N. 2004. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N. Engl. J. Med., 351(27):2817-26. Epub 2004 Dec 10.
10. Ritchie, M.E., Diyagama, D., Neilson, J., van Laar. R., Dobrovic, A., Holloway, A. and Smyth, G.K. 2006. Empirical array quality weights in the analysis of microarray data. BMC Bioinformatics, 7(1):261.
11. Sauer, U., Preininger, C. and Hany-Schmatzberger, R. 2005. Quick and simple: quality control of microarray data. Bioinformatics, 21(8):1572-8.
12. Sharma, P., Sahni, N.S., Tibshirani, R., Skaane, P., Urdal, P., Berghagen, H., Jensen, M., Kristiansen, L., Moen, C., Sharma, P., Zaka, A., Arnes, J., Sauer, T., Akslen, L.A., Schlichting, E., Borresen-Dale, A.L. and Lonneborg, A. 2005. Early detection of breast cancer based on gene-expression patterns in peripheral blood cells. Breast Cancer Res., 7(5):R634-44. Epub 2005 Jun 14.
13. Shi, L., Tong, W., Goodsaid, F., Frueh, F.W., Fang, H., Han, T., Fuscoe, J.C. and Casciano, D.A. 2004. QA/QC: challenges and pitfalls facing the microarray community and regulatory agencies. Expert. Rev. Mol. Diagn., 4(6):761-77.
14. Tran, P.H., Peiffer, D.A., Shin, Y., Meek, L.M., Brody, J.P. and Cho, K.W. 2002. Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals. Nucleic Acids Res., 30(12):e54.
15. Tusher, V.G., Tibshirani, R. and Chu, G. 2001. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. U.S.A., 98(9):5116-21.
16. Wang, X., Ghosh, S. and Guo, S.W. 2001. Quantitative quality control in microarray image processing and data acquisition. Nucleic Acids Res., 29(15):E75-5.