Microarray data quality - Review of current developments

OMICS A Journal of Integrative Biology

Volumn 11, Issue 1, 2007, Pages 1-13

  Wilkes, Timothy ^a   Laux, Holger ^a   Foy, Carole A ^a  

^a LGC   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

DATA ANALYSIS; DNA MICROARRAY; GENE EXPRESSION PROFILING; INFORMATION PROCESSING; INSTRUMENT VALIDATION; MICROARRAY ANALYSIS; PRIORITY JOURNAL; PROCESS DEVELOPMENT; QUALITY CONTROL; REVIEW; SENSITIVITY AND SPECIFICITY;

ANIMALS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENETIC TECHNIQUES; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN ARRAY ANALYSIS; QUALITY CONTROL; RNA;

EID: 34247195100     PISSN: 15362310     EISSN: None     Source Type: Journal    
DOI: 10.1089/omi.2006.0001     Document Type: Review

References (47)

1. ARCHER, K.J., DUMUR, C.L., JOEL, S.E., and RAMAKRISHNAN, W. (2006). Assessing the quality of hybridised RNA in Affymetrix Gene Chip experiments using mixed effects models. Biostatistics 7, 198-212; Aug 31, epub. 2005.
2. BARRETT, J.C., and KAWASAKI, E.S. (2003). Microarrays: the use of oligonucleotides and cDNA for the analysis of gene expression. Drug Discov. Today 8, 134-141.
3. BENJAMINI, Y., and HOTCHBERG, Y. (1995). Controlling the false discovery rate: apractical and powerful approach to multiple testing. JR Statis. Soc. B. 57, 289-300.
4. BRAZMA, A., HINGAMP, P., QUACKENBUSH, J., SHERLOCK, G., SPELLMAN, P., STOECKERT, C., et al. (2001). Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet. 29, 365-371.
5. BROWN, P.O., and BOTSTEIN, D. (1999). Exploring the new world of the genome with DNA microarrays. Nat. Genet. 21, 33-37.
6. 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.
7. BURGOON, L.D., ECKEL-PASSOW, J.E., GENNINGS, C., BOVERHOF, D.R., BURT, J.W., FONG, C.J., et al. (2005). Protocols for the assurance of microarray data quality and process control. Nucleic Acids Res. 33, e172.
8. DRAGHICI, S., KHATRI, P., EKLUND, A.C., and SZALLASI, Z. (2006). Reliability and reproducibility issues in DNA microarray measurements. Trends Genet. 22, 101-109.
9. DUGGAN, D.J., BITTNER, M., CHEN, Y., MELTZER, P., and TRENT, J.M. (1999). Expression profiling using cDNA arrays. Nat. Genet. 21, 10-14.
10. DUMUR, C.L., NASIM, S., BEST, A.M., ARCHER, K.J., LADD, A.C., MASS, V.R., et al. (2004). Evaluation of quality control criteria for microarray gene expression analysis. Clin Chem 50, 1994-2002.
11. FAN, J., TAM, P., WOUDE, G.V., and REN, Y. (2004). Normalization and analysis of cDNA microarrays using within-array replications applied to neuroblastoma cell response to a cytokine. Proc. Natl. Acad. Sci. USA 101, 1135-1140.
12. GOLLUB, J., BALL, C.A., BINKLEY, G., DEMETER, J., FINKELSTEIN, D.B., HEBERT, J.M. et al. (2003). The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res. 31, 94-96.
13. HALGREN, R.G., FIELDEN, M.R., FONG, C.J., and ZACHAREWSKI, T.R. (2001). Assessment of clone identity and sequence fidelity for 1189 IMAGE cDNA clones. Nucleic Acids Res. 29, 582-588.
14. HARDIMAN, G. (2004). Microarray platforms-comparisons and contrasts. Pharmacogenomics 5, 487-502.
15. HELD, A.G., GRINSTEIN, G., and TU, Y. (2006). Relationship between gene expression and observed intensities in DNA microarrays - a modelling study. Nucleic Acids Res. 34, e70.
16. HESSNER, M.J., MEYER, L., TACKES, J., MUHEISEN, S., and WANG, X. (2004). Immobilized probe and glass surface chemistry as variables in microarray fabrication. BMC Genomics 5, 53.
17. HESSNER, M.J., WANG, X., KHAN, S., MEYER, L., SCHLICHT, M., TACKES, J., et al. (2003). Use of a three-color cDNA microarray platform to measure and control support-bound probe for improved data quality and reproducibility. Nucleic Acids Res. 31, e60.
18. IMBEAUD, S., and AUFFRAY, C. (2005). 'The 39 steps' in gene expression profiling: critical issues and proposed best practices for microarray experiments. Drug Discov. Today 10, 1175-1182.
19. JARVINEN, A.K., HAUTANIEMI, S., EDGREN, H., AUVINEN, P., SAARELA, J., KALLIONIEMI, O., et al. (2004). Are data from different gene expession microarray platforms comparable? Genomics 83, 1164-1168.
20. JENSSEN, T.K., LANGAAS, M., KUO, W.P., SMITH-SORENSEN, B., MYKLEBOST, O., and HOVIG, E. (2002). Analysis of repeatability in spotted cDNA microarrays. Nucleic Acids Res. 30, 3235-3244.
21. JONES, L., GOLDSTEIN, D.R., HUGHES, G.P., STRAND, A., COLLIN, F., DUNNETT, S.B., et al. (2006). Assessment of the relationship between pre-chip and post-chip quality measures for Affymetrix expression data. BMC Bioinformatics 7, 211, doi.10.1186/1471-2105-7-211.
22. KANE, M.D., JATKOE, T.A., STUMPF, C.R., LU, J., THOMAS, J.D., and MADORE, S.J. (2000). Assessment of the sensitivity and specificity of oligonucleotide (50 mer) arrays. Nucleic Acid Res. 28, 4552-4557.
23. KIM, K., PAGE, G.P., BEASLEY, T.M., BARNES, S., SCHEIRER, K.E., and ALLISON, D.B. (2006). A proposed metric for assessing the measurement quality of individual microarrays. BMC Bioinformatics 7, 35.
24. KNAPINSKA, A.M., IRISZARRY-BARRETO, P., ADUSUMALLI, S., and BREWER, G. (2005). Molecular mechanisms regulating mRNA stability: physiological and pathological significance. Curr. Genom. 6, 471-486.
25. KONIG, R., BALDESSARI, D., POLLET, N., NIEHRS, C., and EILS, R. (2004). Reliability of gene expression ratios for cDNA microarrays in multiconditional experiments with a reference design. Nucleic Acids Res. 32, e29.
26. KOPTHAPALLI, R., YODER, S.J., MANE, S., and LOUGHRAN, T.P. (2002). Microarray results, how accurate are they? Bioinformatics 3, 22.
27. KUO, W.P., JENSENN, T.K., BUTTE, A.J., OHNO-MACHADO, L., and KOHANE, I.S. (2002). Analysis of matched RNA measurements from two different microarray technologies. Bioinformatics 18, 405-412.
28. LIPSHUTZ, R.J., FODOR, S.P.A., GINGERAS, T.R., and LOCKHART, D.J. (1999). High density synthetic oligonucleotide arrays. Nat. Genet. 21, 20-24.
29. PAGE, G.P., EDWARDS, J.P., BARNES, S., WEINDRUCH, R., and ALLISON, D.B. (2003). A design and statistical perspective on micro array gene expression studies in nutrition: the need for playful creativity and scientific hard-mindedness. Nutrition 19, 997-1000.
30. PETRI, A., FLECKNER, J., and MATTHIESSEN, M.W. (2004). Array-A-Lizer: a serial DNA microarray quality analyzer. BMC Bioinformatics 5, 12.
31. RAIKHEL, N., and SOMERVILLE, S. (2004). Modification of the data release policy for gene expression profiling experiments. Plant Physiol. 135, 1149.
32. SCHENA, M., SHALON, D., DAVIS, R.W., and BROWN, P.O. (1995). Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470.
33. SHI, L., FRUEH, F.W., SCHERF, U., PURI, R.K., JACKSON, S.A., HARBOTTLE, H.C., et al. (2005). The MAQC (Micro array Quality Control) Project: calibrated RNA samples reference datasets, and QC metrics and thresholds. In the 11th Annual FDA Science Forum: Advancing Public Health Through Innovative Science, April 27-28, 2005, Washington D.C., D11.
34. SMYTH, G.K., and SPEED, T. (2003). Normalization of cDNA microarray data. Methods 31, 265-373.
35. SPRUILL, S.E., LU, J., HARDY, S., and WEIR, B. (2002). Assessing sources of variability in microarray gene expression data. Biotechniques 33, 916-923.
36. STEINFATH, M., WRUCK, W., SEIDEL, H., LEHRACH, H., RADELOF, U., and O'BRIEN, J. (2001). Automated image analysis for array hybridization experiments. Bioinformatics 7, 634-641.
37. TAN, P.K., DOWNEY, T.J., SPITZNAGEL, E.L., XU, P., FU, D., DIMITROV, D.S., et al. (2003). Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res. 31, 5676-5684.
38. TOMITA, H., VAWTER, M.P., WALSH, D.M., EVANS, S.J., CHOUDARY, P.V., OVERMAN, K.M., et al. (2004). Effect of agonal and postmortem factors on gene expression profile: quality control in microarray analyses of postmortem human brain. Biol. Psych. 55, 346-352.
39. 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, e54.
40. TSENG, G.C., OH, M.K., ROHLIN, L., LIAO, J.C., and WONG, W.H. (2001). Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res. 29, 2549-2557.
41. WANG, X., GHOSH, S., and GUO, S.W. (2001). Quantitative quality control in microarray image processing and data acquisition. Nucl. Acids Res. 29, e75.
42. WANG, X., HESSNER, M.J., WU, Y., PATI, N., and GHOSH, S. (2003). Quantitative quality control in microarray experiments and the application in data filtering, normalization and false positive rate prediction. Bioinformatics 19, 1341-1347.
43. WILDSMITH, S.E., ARCHER, G.E., WINKLEY, A.J., LANE, P.W., and BUGELSKI, P.J. (2001). Maximization of signal derived from cDNA microarrays. Biotechniques 30, 202-206, 208.
44. YANG, I.V., CHEN, E., HASSEMAN, J.P., LIANG, W., FRANK, B.C., WANG, S., et al. (2002). Within the fold: assessing differential expression measures and reproducibility in microarray assays. Genome Biol. 3 research0062; epub Oct. 24, 2002.
45. YANG, Y.H., DUDOIT, S., LUU, P., LIN, D.M., PENG, V., NGAI, J., et al. (2002). Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30, e15.
46. YANG, M.C., RUAN , Q.G., YANG, J.J., ECKENRODE, S., WU, S., MCINDOE, R.A., et al. (2001). A statistical method for flagging weak spots improves normalization and ratio estimates in microarrays. Physiol. Genom. 7, 45-53.
47. YOUNG, R.A. (2000). Biomedical discovery with DNA arrays. Cell 102, 9-15.