Comparison of different probe-level analysis techniques for oligonucleotide microarrays

作者: Barbara Rosati , Frederic Grau , Anneke Kuehler , Samantha Rodriguez , David McKinnon

DOI: 10.2144/04362MT03

关键词:

摘要: Three different software packages for the probe-level analysis of high-density oligonucleotide microarray data were compared using an experiment-derived set that was validated real-time PCR. The efficiency with which these three programs could identify true positives in this assessed. In addition, estimates false-positive and false-negative rates determined. performance very small sets also compared, recommendations use are suggested.

参考文章(8)
Rafael A. Irizarry, Laurent Gautier, Leslie M. Cope, An R Package for Analyses of Affymetrix Oligonucleotide Arrays Statistics for Biology and Health. pp. 102- 119 ,(2003) , 10.1007/0-387-21679-0_4
Ross Ihaka, Robert Gentleman, R: A Language for Data Analysis and Graphics Journal of Computational and Graphical Statistics. ,vol. 5, pp. 299- 314 ,(1996) , 10.1080/10618600.1996.10474713
Jeanne M. Nerbonne, David McKinnon, Frederic Grau, Samantha Rodriguez, Barbara Rosati, Huilin Li, Concordant expression of KChIP2 mRNA, protein and transient outward current throughout the canine ventricle. The Journal of Physiology. ,vol. 548, pp. 815- 822 ,(2003) , 10.1111/J..2003.T01-1-00815.X
C. Li, W. H. Wong, Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection Proceedings of the National Academy of Sciences of the United States of America. ,vol. 98, pp. 31- 36 ,(2001) , 10.1073/PNAS.98.1.31
Rafael A Irizarry, Benjamin M Bolstad, Francois Collin, Leslie M Cope, Bridget Hobbs, Terence P Speed, Summaries of Affymetrix GeneChip probe level data Nucleic Acids Research. ,vol. 31, ,(2003) , 10.1093/NAR/GNG015
B.M. Bolstad, R.A Irizarry, M. Astrand, T.P. Speed, A comparison of normalization methods for high density oligonucleotide array data based on variance and bias Bioinformatics. ,vol. 19, pp. 185- 193 ,(2003) , 10.1093/BIOINFORMATICS/19.2.185