Quantitative quality control in microarray image processing and data acquisition

Nucleic Acids Research

Volumn 29, Issue 15, 2020, Pages

  Wang, Xujing ^a   Ghosh, Soumitra ^a   Guo, Sun Wei ^a  

^a CHILDREN S HOSPITAL OF WISCONSIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA MICROARRAY; FILTRATION; IMAGE PROCESSING; QUALITY CONTROL; RELIABILITY; ALGORITHM; COMPUTER PROGRAM; METHODOLOGY; REGRESSION ANALYSIS; REPRODUCIBILITY;

ALGORITHMS; LEAST-SQUARES ANALYSIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; QUALITY CONTROL; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 0035433128     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/29.15.e75     Document Type: Article

References (16)

1. Brown, P.O. and Botstein, D. (1999) Exploring the new world of the genome with DNA microarrays. Nature Genet., 21 (suppl. 1), 33-37.
2. Debouck, C. and Goodfellow, P.N. (1999) DNA microarrays in drug discovery and development. Nature Genet., 21 (suppl. 1), 48-50.
3. Khan, J., Bittner, M.L., Chen, Y., Meltzer, P.S. and Trent, J.M. (1999) DNA microarray technology: the anticipated impact on the study of human disease. Biochim. Biophys. Acta, 1423, M17-M28.
4. Diehn, M., Alizadeh, A.A. and Brown, P.O. (2000) Examining the living genome in health and disease with DNA microarrays. J. Am. Med. Assoc., 283, 2298-2299.
5. Eisen, M.B., Spellman, P.T., Brown, P.O. and Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA, 95, 14863-14868.
6. Tamayo, P., Slonim, D., Mesirov, J., Zhu, Q., Kitareewan, S., Dmitrovsky, E., Lander, E.S. and Golub, T.R. (1999) Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc. Natl Acad. Sci. USA, 96, 2907-2912.
7. Zhang, M.Q. (1999) Large-scale gene expression data analysis: a new challenge to computational biologists. Genome Res., 9, 681-688. (Erratum, Genome Res., 1999, 9, 1156]
8. Schena, M., Shalon, D., Heller, R., Chai, A., Brown, P.O. and Davis, R.W. (1996) Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc. Natl Acad. Sci. USA, 93, 10614-10619.
9. Chen, Y., Dougherty, E.R. and Bittner, M.L. (1997) Ratio-based decisions and the quantitative analysis of cDNA microarray images. J. Biomed. Optics, 2, 364-374.
10. Zhou, Y.-X., Kalocsai, P., Chen, J.-Y. and Shams, S. (2000) Information processing issues and solutions associated with microarray technology. In Schena, M. (ed.), Microarray Biochip Technology. Bio Techniques Books, Natick, MA, pp. 167-200.
11. Lee, M.L., Kuo, F.C., 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.
12. 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, 531-537.
13. Manduchi, E., Grant, G.R., Mc Kenzie, S.E., Overton, G.C., Surrey, S. and Stoeckert, C.J., Jr (2000) Generation of patterns from gene expression data by assigning confidence to differentially expressed genes. Bioinformatics, 16, 685-698.
14. De Risi, J., Penland, L., Brown, P.O., Bittner, M.L., Meltzer, P.S., Ray, M., Chen, Y., Su, Y.A. and Trent, J.M. (1996) Use of a cDNAmicroarray to analyse gene expression patterns in human cancer. Nature Genet., 14, 457-460.
15. Khan, J., Simon, R., Bittner, M.L., Chen, Y., Leighton, S.B., Pohida, T., Smith, P.D., Jiang, Y., Gooden, G.C., Trent, J.M. and Meltzer, P.S. (1998) Gene expression profiling of alveolar rhabdomyosarcoma with cDNA microarrays. Cancer Res., 58, 5009-5013.
16. Tavazoie, S., Hughes, J.D., Campbell, M.J., Cho, R.J. and Church, G.M. (1999) Systematic determination of genetic network architecture. Nature Genet., 22, 281-285.