Comparison of different probe-level analysis techniques for oligonucleotide microarrays

BioTechniques

Volumn 36, Issue 2, 2004, Pages 316-322

  Rosati, Barbara ^a   Grau, Frederic ^a   Kuehler, Anneke ^a   Rodriguez, Samantha ^a   McKinnon, David ^a  

^a STONY BROOK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SOFTWARE; DATA REDUCTION; REAL TIME SYSTEMS;

DATA SETS; MICROARRAYS;

NUCLEIC ACIDS;

DNA; OLIGONUCLEOTIDE;

ACCURACY; ANALYTIC METHOD; ANALYTICAL ERROR; ANIMAL TISSUE; ARTICLE; COMPUTER PROGRAM; DATA ANALYSIS; DIAGNOSTIC VALUE; DNA MICROARRAY; DNA PROBE; INTERMETHOD COMPARISON; LABORATORY DIAGNOSIS; NONHUMAN; PERFORMANCE; RAT; REAL TIME POLYMERASE CHAIN REACTION; VALIDATION PROCESS;

ANIMALIA;

EID: 0842309817     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/04362mt03     Document Type: Article

References (9)

1. Affymetrix Technical Report. 2001. Statistical algorithms reference guide. Affymetrix, Santa Clara, CA, USA.
2. Li, C. and W.H. Wong. 2001. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. USA 98:31-36.
3. Li, C. and W.H. Wong. 2001. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biology 2:research0032.1-0032.11.
4. Bolstad, B.M., R.A. Irizarry, M. Astrand, and T.P. Speed. 2003. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19:185-193.
5. Irizarry, RA, L. Gautier, and L. Cope. 2003. An R Package for Analyses of Affymetrix Oligonucleotide Arrays, p. 45-52. In G. Parmigiani, E.S. Garrett, R.A. Irizarry, and S.L. Zeger (Eds.), The Analysis of Gene Expression Data: Methods and Software. Springer, Berlin.
6. Dixon, J.E. and D. McKinnon. 1994. Quantitative analysis of potassium channel mRNA expression in atrial and ventricular muscle of rats. Circ. Res. 75:252-260.
7. Ihaka, R. and R. Gentleman. 1996. R: A language for data analysis and graphics. J. Comput. Graph. Stat. 5:299-314.
8. Irizarry, R.A., B.M. Bolstad, F. Collin, L.M. Cope, B. Hobbs, and T.P. Speed. 2003. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31:e15.
9. Rosati, B., F. Grau, S. Rodriguez, H. Li, J.M. Nerbonne, and D. McKinnon. 2003. Concordant expression of KChIP2 mRNA, protein and transient outward current throughout the canine ventricle. J. Physiol. 548:815-822.