OLIN: Optimized normalization, visualization and quality testing of two-channel microarray data

Bioinformatics

Volumn 21, Issue 8, 2005, Pages 1724-1726

  Futschik, Matthias E ^a,b   Crompton, Toni ^c  

^a HUMBOLDT UNIVERSITY   (Germany)

^b UNIVERSITY OF OTAGO   (New Zealand)

^c UNIVERSITY OF OTAGO   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANALYTICAL ERROR; ARTICLE; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA ANALYSIS; DEVICE; DNA MICROARRAY; EXPERIMENT; PRIORITY JOURNAL; QUALITY CONTROL; REGRESSION ANALYSIS;

EID: 17444399363     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti199     Document Type: Article

References (9)

1. Futschik,M. and Crompton,T. (2004) Model selection and efficiency testing for normalisation of cDNA microarray data. Genome Biol., 5, R60.
2. Futschik,M., Jeffs,A., Pattison,S., Kasabov,N., Sullivan,M. and Reeve,A. (2002) Gene expression profiling of metastatic and nonmetastatic colorectal cancer cell lines. Genome Lett., 1, 26-33.
3. Gentleman,R.C., Carey,V.J., Bates,D.M., Bolstad,B., Dettling,M., Dudoit,S., Ellis,B., Gautier,L., Ge,Y., Gentry,J. et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5, R80.
4. Hoffmann,R., Seidl,T. and Dugas,M. (2002) Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis. Genome Biol., 3, research0033.1-research0033.11.
5. Holloway,A.J., van Laar,R.K., Tothill,R.W. and Bowtell,D. (2002) Options available-from start to finish-for obtaining data from DNA microarrays II. Nat. Genet., 32 (Suppl. 2), 481-489.
6. Ihaka,R. and Gentleman,R. (1996) R: a language of data analysis and graphics. J. Comput. Graphic Stat., 5, 299-314.
7. Loader,C. (1999) Local Regression and Likelihood. Springer, NY.
8. Quackenbush,J. (2002) Microarray data normalization and transformation. Nat. Genet., 32 (Suppl. 2), 496-501.
9. Yang,Y.H., Dudoit,S., Luu,P., Lin,D.M., Peng,V., Ngai,J. and Speed,T. (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple systematic variation. Nucleic Acids Res., 30, e15.