An overview of image-processing methods for affymetrix genechips

Briefings in Bioinformatics

Volumn 9, Issue 1, 2008, Pages 25-33

  Arteaga Salas, Jose M ^a   Zuzan, Harry ^a   Langdon, William B ^a   Upton, Graham J G ^a   Harrison, Andrew P ^a  

^a UNIVERSITY OF ESSEX   (United Kingdom)

Author keywords

Affymetrix microarrays; Image processing

Indexed keywords

ACCURACY; ANALYTICAL ERROR; ARTIFACT; AUTOMATED PATTERN RECOGNITION; COLON CANCER; COMPUTER PROGRAM; EXON; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE TECHNOLOGY; GENETIC ALGORITHM; HUMAN; IMAGE PROCESSING; IMAGE QUALITY; INFORMATION PROCESSING; MICROARRAY ANALYSIS; MICROCHIP ANALYSIS; QUALITY CONTROL; REFERENCE VALUE; RELIABILITY; REVIEW; ROC CURVE; SENSITIVITY ANALYSIS; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; ALGORITHM; COMPUTER ASSISTED DIAGNOSIS; DNA MICROARRAY; FLUORESCENCE IN SITU HYBRIDIZATION; IMAGE ENHANCEMENT; METHODOLOGY; MULTIPHOTON MICROSCOPY;

ALGORITHMS; GENE EXPRESSION PROFILING; IMAGE ENHANCEMENT; IMAGE INTERPRETATION, COMPUTER-ASSISTED; IN SITU HYBRIDIZATION, FLUORESCENCE; MICROSCOPY, FLUORESCENCE, MULTIPHOTON; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 38049173235     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbm055     Document Type: Review

References (22)

1. Barrett T, Suzek T, Troup D, et al. NCBI GEO: Mining millions of expression profiles-database and tools. Nucleic Acids Res 2005; 33:D562-6.
2. Gentleman R, Carey V, Huber W, et al. Quality assessment of Affymetrix GeneChip Data, in Bioinformatics and Computational Biology Solutions Using R and Bioconductor, Springer, 2005.
3. Schadt EE, Li C, Ellis B, Wong WH. Feature extraction and normalization algorithms for high-density oligonucleotide gene expression data. J Cell Bio Supplement 2001;37:120-5.
4. Zuzan H., Blanchette C., Dressman H. et al. [http://ftp.stat.duke.edu/WorkingPapers/02-05.pdf]
5. Baggerly K.A. [http://www.mdanderson.org/pdf/biostats_utmdabtr00503.pdf]
6. Hekstra D, Taussig AR, Magnasco M, Naef F. Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays. Nucleic Acids Res 2003;31:1962-8.
7. Naef F, Magnasco M. Solving the riddle of the bright mismatches. Phys Rev E 2003;68:011906.
8. Suárez-Fariña M, Pellegrino M, Wittkowski K, Magnasco M. Harshlight: A corrective make-up program for microarray chips. BMC Bioinformatics 2005;6:294.
9. Upton GJG, Lloyd JC. Oligonucleotide arrays: Information from replication and spatial structure. Bioinformatics 2005;21: 4162-8.
10. Bolstad BM, Collin F, Brettschneider J, et al. Quality assessment of Affymetrix GeneChip Data. In: Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S, (eds). Bioinformatics and Computational Biology Solutions Using R and Bioconductor, Springer, 2005;33-47.
11. Bolstad B. Website: http://plmimagegallery.bmbolstad.com/index.html, (7 November 2007, date last accessed)
12. Reimers M, Weinstein JN. Quality assessment of microarrays: Visualization of spatial artefacts and quantitation of regional biases. BMC Bioinformatics 2005;6:166.
13. AffyWebdata: Affymetrix Website. http://www.affymetrix.com/support/ technical/sample_data/datasets.affx, (7 November 2007, date last accessed)
14. Suárez-Fariña M, Haider A, Wittkowski K. Harshlighting small blemishes on microarrays. BMC Bioinformatics 2005;6:65.
15. Cormen TH, Leiserson CE, Rivest RL, Stein C. Introduction to algorithms: 2nd edition. Cambridge, MA: The MIT Press, 2001
16. Russ JC. The Image Processing Handbook: 4th Edition, Boca Raton, FL: CRC Press, 2002.
17. Song J, Maghsoudi K, Li W, et al. Microarray blob-defect removal improves array analysis. Bioinformatics 2007;23: 966-71.
18. Hubbell E, Liu W, Mei R. Robust estimators for expression analysis. Bioinformatics 2002;18:1585-92.
19. Wu Z, Irizarry RA, Gentleman R, et al. A model based background adjustment for oligonucleotide expression arrays. J Am Stat Assoc 2004;99:909-17.
20. Irizarry RA, Bolstad BM, Collin F, et al. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003;31:15.
21. Cope LM, Irizarry RA, Jaffee HA, et al. A benchmark for Affymetrix GeneChip expression measures. Bioinformatics 2004;20:323-31.
22. Arteaga-Salas J.M. and Upton GJG. A normalisation method for oligonucleotide arrays motivated by spatial biases. Proceedings of the 26th Leeds Annual Statistical Research Workshop, University of Leeds, 2007; 26, pp. 95-8.