Methods for estimating and mitigating errors in spotted, dual-color DNA microarrays

OMICS A Journal of Integrative Biology

Volumn 11, Issue 2, 2007, Pages 186-199

  Karakach, Tobias K ^a   Wentzell, Peter D ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DNA; MESSENGER RNA;

ANALYTICAL ERROR; ARTICLE; DATA ANALYSIS; DNA MICROARRAY; MEASUREMENT; METHODOLOGY; MICROARRAY ANALYSIS; MODEL; NONHUMAN; PRIORITY JOURNAL; STATISTICAL ANALYSIS; TECHNOLOGY;

ANALYSIS OF VARIANCE; COMPUTATIONAL BIOLOGY; DATA INTERPRETATION, STATISTICAL; DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; LINEAR MODELS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 34347344984     PISSN: 15362310     EISSN: None     Source Type: Journal    
DOI: 10.1089/omi.2007.0008     Document Type: Article

References (46)

1. ALIZADEH, A.A., EISEN, M.B., DAVIS, R.E., MA, C., LOSSOS, I.S., ROSSENWALD, A., et al. (2000). Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403, 503-511.
2. BRODY, P.J., WILLIAMS, B.A., WOLD, B.J., and QUAKE, S.R. (2002). Significance and statistical error in the analysis of DNA microarray data. Proc Natl Acad Sci USA 99, 12975-12978.
3. BROWN, C.S., GOODWIN, P.C., and SORGER, P. K. (2001). Image metrics in the statistical analysis of DNA microarray data. Proc Natl Acad Sci USA 98, 8944-8949.
4. CHEN, Y., DOUGHERTY, E.R., and BITTNER, M.L. (1997). Ratio-based decisions and the quantitative analysis of cDNA microarray images. J Biomed Opt 2, 364-374.
5. 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, 1207-1215.
6. CHURCHILL, G.A. (2002). Fundamentals of experimental design for cDNA microarray experiments. Nat Genet (Suppl) 32, 490-494.
7. DOBBIN, K., and SIMON, R. (2002). Comparison of microarray designs for class comparison and class discovery. Bioinformatics 18, 1438-1445.
8. DOBBIN, K., SHIH, J.H., and SIMON, R. (2003). Statistical design of reverse dye microarrays. Bioinformatics 19, 803-810.
9. DRAGHICI, S., KHATRI, P., EKLUND, A.C., and SZALLASI, Z. (2006). Reliability and reproducibility issues in DNA microarray measurements. Trends Genet 22, 101-109.
10. DURBIN, B.P., HARDIN, J.S., HAWKINS, D.M., and ROCKE, D.M. (2002). A variance stabilizing transformation for gene-expression microarray data. Bioinformatics 18, S105-S110.
11. DURBIN, B.P., and ROCKE, D.M. (2004). Variance-stabilizing transformations for two-color microarrays. Bioinformatics 20, 660-667.
12. EFRON, B., and TIBSHIRANI, R. (2002). Empirical bayes methods and false discovery rates for microarrays. Genet Epidemiol 23, 70-86.
13. EFRON, B., TIBSHIRANI, R., STOREY, J.D., and TUSHER, V. (2001). Empirical bayes analysis of a microarray experiment. J Am Stat Assoc 96, 1151-1160.
14. GORYACHEV, A.B., MACGREGOR, P.F., and EDWARDS, A.M. (2001). Unfolding of microarray data. J Comput Biol 8, 443-461.
15. HUBER, W., VON HEYDEBRECK, A., SULTMANN, H., POUSTKA, A., and VINGRON, M. (2002). Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18, S96-S104.
16. IDEKER, T., THORSSON, V., SEIGEL, A.F., and HOOD, L.E. (2000). Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data. J Comput Biol 7, 805-817.
17. JENSSEN, T.K., LANGAAS, M., KUO, W.P., SMITH-S RENSEN, B., MYKLEBOST, O., and HOVIG, E. (2002). Analysis of repeatability in spotted cDNA microarrays. Nucleic Acids Res 30, 3235-3244.
18. KADOTA, K., MIRI, R., BONO, H., SHIMIZU, K., OKAZAKI, Y., and HAYASHIKAZI, Y. (2001). Preprocessing implementation for microarray (PRIM): an efficient method for processing cDNA microarray data. Physiol Genomics 4, 183-188.
19. KERR, M.K., MARTIN, M., and CHURCHILL, G.A. (2000). Analysis of variance for gene expression microarray data. J Comput Biol 7, 819-837.
20. KERR, M.K., and CHURCHILL, G.A. (2001). Experimental design for gene expression microarrays. Biostatistics 2, 183-201.
21. KHONDOKER, M.R., GLABEY, C.A., and WOUDE, G.V. (2006). Statistical estimation of gene expression using multiple laser scans of microarrays. Bioinformatics 22, 215-219.
22. KIM, S.B., RHA, S.Y., CHO, G.B., and CHUNG, H.C. (2004). Spearman's footrule as a measure of cDNA microarray reproducibility. Genomics 84, 441-448.
23. KOTHAPALLI, R., YODER, S.J., MANE, S., and LOUGHRAN JR., T. P. (2002). Microarray results: How accurate are they? BMC Bioinformatics 3, 22.
24. KUO, W.P., JENSSEN, T.K., BUTTE, A.J., OHNO-MACHADO, L., and KOHANE, I.S. (2002). Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 18, 405-412.
25. LARKIN, E.J., FRANK, C.B., GAVRAS, H., SULTANA, R., and QUACKENBUSH, J. (2005). Independence and reproducibility across microarray platforms. Nat Methods 5, 337-343.
26. LEE, M.L.T., KUO, C.F., WHITMORE, G.A., and SKLAR, J. (2000). Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl Acad Sci USA 97, 9834-9839.
27. NEWTON, M.A., KENDZIORSKI, CM., RICHMOND, C.S., BLATTNER, F.R., and TSUI, K.W. (2001). On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data. J Comput Biol 8, 37-52.
28. PAN, W. (2002). A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. Bioinformatics 18, 546-554.
29. PAN, W., LIN, J., and LE, T.C. (2002). How many replicates of arrays are required to detect gene expression changes in microarray experiments? A mixture model approach. Genome Biol 3, researcb.0022.1-0022.10.
30. QUACKENBUSH, J. (2002). Microarray data normalization and transformation. Nat Genet (Suppl) 32, 496-501.
31. RAFFELSBERGER, W., DEMBÉLÉ, D., NEUBAUER, M.G., GOTTARDIS, M.M., and GRONEMEYER, H. (2002). Quality indicators increase the reliability of microarray data. Genomics 80, 385-394.
32. ROCKE, D.M., and DURBIN, B. (2001). A model for measurement error for gene expression arrays. J Comput Biol 8, 557-569.
33. ROCKE, D.M., and DURBIN, B. (2003). Approximate variance-stabilizing transformations for gene-expression microarray data. Bioinformatics 19, 966-972.
34. ROMUALDI, C., TREVISAN, S., CELEGATO, B., COSTA, G., and LANFRANCHI, G. (2003). Improved detection of differentially expressed genes in microarray experiments though multiple scanning and image integration. Nucleic Acids Res 31, e149.
35. SAUER, U., PREININGER, C., and HANY-SCHMATZBERGER, R. (2005). Quick and simple: quality control of microarray data. Bioinformatics 21, 1572-1578.
36. SCHENA, M., SHALON, D., DAVIS, D.W., and BROWN, P.O. (1995). Quantitative monitoring of gene expression patterns with a complementary DNA. Science 270, 467-470.
37. SCHUCHHARDT, J., BEULE, D., MALIK, A., WOLSKI, E., EICKHOFF, H., LEHRACH, H., et al. (2000). Normalization strategies for cDNA microarrays. Nucleic Acids Res 28, e47.
38. SIMON, R.M., and DOBBIN, K. (2003). Experimental design of DNA microarray experiments. Biotechniques 34, S16-S21.
39. THOMAS, J.G., OLSON, J.M., TAPSCOT, S.J., and ZHAO, L.P. (2001). An efficient and robust statistical modeling approach to discover differentially expressed genes using genomic expression profiles. Genome Res 11, 1227-1236.
40. TRAN, P.H., PEIFFER, D.A., SHIN, Y., MEEK, L.M., BRODY, P.J., and CHO, K.W.Y. (2002). Microarray optimization: increasing spot accuracy and automated identification of true microarray signals. Nucleic Acids Res 30, e54.
41. TSENG, G.C., OH, M.K., LIAO, J.C., and WONG, W. H. (2001). Issues in cDNA microarray analysis: quality filter-ing, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res 29, 2549-2557.
42. TUSHER, V.G., TIBSHIRANI, R., and CHU, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98, 5116-5121.
43. VINCIOTTI, V., KHANIN, R., D'ALIMONTE, D., LIU, X., CATTINI, N., HOTCHKISS, G., et al. (2005). An experimental evaluation of a loop versus a reference design for two-channel microarrays. Bioinformatics 21, 492-501.
44. WANG, X., GHOSH, S., and GUO, S.W. (2001). Quantitative quality control in microarray image processing and data acquisition. Nucleic Acids Res 29, e75.
45. WOLFINGER, R.D., GIBSON, G., WOLFINGER, E.D., BENNETT, L., HAMADEH, H., BUSHEL, P., et al. (2001). Assesing gene significance from cDNA microarray expression data via mixed models. J Comput Biol 8, 625-637.
46. YANG, H.Y., and SPEED, T.P. (2002). Design issues for cDNA microarray experiments. Nat Rev Genet 3, 579-588.