Protocols for the assurance of microarray data quality and process control

Nucleic Acids Research

Volumn 33, Issue 19, 2005, Pages 1-11

  Burgoon, L D ^a,c   Eckel Passow, J E ^d   Gennings, C ^e   Boverhof, D R ^b,c   Burt, J W ^b,c   Fong, C J ^b,c   Zacharewski, T R ^b,c  

^a MICHIGAN STATE UNIVERSITY   (United States)

^b Michigan State University   (United States)

^c MICHIGAN STATE UNIVERSITY   (United States)

^d MAYO CLINIC CANCER CENTER   (United States)

^e VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ACCURACY; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; DATA ANALYSIS; DNA MICROARRAY; IN VITRO STUDY; IN VIVO STUDY; PREDICTION; PRIORITY JOURNAL; PROCESS CONTROL; QUALITY CONTROL; VALIDATION PROCESS; ARTIFICIAL INTELLIGENCE; COLOR; GENE EXPRESSION PROFILING; KINETICS; METHODOLOGY; REGRESSION ANALYSIS; REPRODUCIBILITY; STANDARD;

ARTIFICIAL INTELLIGENCE; COLOR; GENE EXPRESSION PROFILING; KINETICS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; QUALITY CONTROL; REGRESSION ANALYSIS; REPRODUCIBILITY OF RESULTS;

EID: 28544432211     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gni167     Document Type: Article

References (17)

1. 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.
2. Jarvinen,A.K., Hautaniemi,S., Edgren,H., Auvinen,P., Saarela,J., Kallioniemi,O.P. and Monni,O. (2004) Are data from different gene expression microarray platforms comparable? Genomics, 83, 1164-1168.
3. Ulrich,R.G., Rockett,J.C., Gibson,G.G. and Pettit,S.D. (2004) Overview of an interlaboratory collaboration on evaluating the effects of model hepatotoxicants on hepatic gene expression. Environ. Health Perspect., 112, 423-427.
4. Miles,M.F. (2001) Microarrays: Lost in a storm of data? Nature Rev. Neurosci., 2, 441-443.
5. Grant,G.R., Manduchi,E., Pizarro,A. and Stoeckert,C.J.,Jr (2003) Maintaining data integrity in microarray data management. Biotechnol. Bioeng., 84, 795-800.
6. Wang,X., Ghosh,S. and Guo,S.W. (2001) Quantitative quality control in microarray image processing and data acquisition. Nucleic Acids Res., 29, E75-5.
7. 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, 2031-2038.
8. Gollub,J., Ball,C.A., Binkley,G., Demeter,J., Finkelstein,D.B., Hebert,J.M., Hernandez-Boussard,T., Jin,H., Kaloper,M., Matese,J.C. et al. (2003) The Stanford Microarray Database: Data access and quality assessment tools. Nucleic Acids Res., 31, 94-96.
9. Petri,A., Fleckner,J. and Matthiessen,M.W. (2004) Array-A-Lizer: A serial DNA microarray quality analyzer. BMC Bioinformatics, 5, 12.
10. Model,F., Konig,T., Piepenbrock,C. and Adorjan,P. (2002) Statistical process control for large scale microarray experiments. Bioinformatics, 18, S155-S163.
11. Yang,Y.H., Dudoit,S., Luu,P., Lin,D.M., Peng,V., Ngai,J. and Speed,T.P. (2002) Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res., 30, e15.
12. Eckel,J.E., Gennings,C., Therneau,T.M., Burgoon,L.D., Boverhof,D.R. and Zacharewski,T.R. (2005) Normalization of two-channel microarray experiments: A semiparametric approach. Bioinformatics, 21, 1078-1083.
13. Boverhof,D.R., Fertuck,K.C., Burgoon,L.D., Eckel,J.E., Gennings,C. and Zacharewski,T.R. (2004) Temporal- and dose-dependent hepatic gene expression changes in immature ovariectomized mice following exposure to ethynyl estradiol. Carcinogenesis, 25, 1277-1291.
14. Sun,Y.V., Boverhof,D.R., Burgoon,L.D., Fielden,M.R. and Zacharewski,T.R. (2004) Comparative analysis of dioxin response elements in human, mouse and rat genomic sequences. Nucleic Acids Res., 32, 4512-4523.
15. Boverhof,D.R., Tam,E., Harney,A.S., Crawford,R.B., Kaminski,N.E. and Zacharewski,T.R. (2004) 2,3,7,8-Tetrachlorodibenzo-p-dioxin induces suppressor of cytokine signaling 2 in murine B cells. Mol. Pharmacol., 66, 1662-1670.
16. Dudoit,S., Yang,H.Y., Callow,M.J. and Speed,T. (2002) Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica Sinica, 12, 111-139.
17. Fare,T.L., Coffey,E.M., Dai,H., He,Y.D., Kessler,D.A., Kilian,K.A., Koch,J.E., LeProust,E., Marton,M.J., Meyer,M.R. et al. (2003) Effects of atmospheric ozone on microarray data quality. Anal. Chem., 75, 4672-4675.