Calibration and assessment of channel-specific biases in microarray data with extended dynamical range

作者: Henrik Bengtsson , Göran Jönsson , Johan Vallon-Christersson

DOI: 10.1186/1471-2105-5-177

关键词: Expression (mathematics)Artificial intelligenceCalibrationGeneticsDNA microarrayProcess (computing)ScannerPattern recognitionCommunication channelRange (mathematics)Microarray analysis techniquesBiology

摘要: Non-linearities in observed log-ratios of gene expressions, also known as intensity dependent log-ratios, can often be accounted for by global biases the two channels being compared. Any step a microarray process may introduce such offsets and this article we study introduced scanner image analysis software.

参考文章(19)
Henrik Bengtsson, aroma - An R object-oriented microarray analysis environment Preprint without journal information; (2004:18) (2004). ,(2004)
Yee Hwa Yang, Natalie P. Thorne, Normalization for two-color cDNA microarray data Institute of Mathematical Statistics. pp. 403- 418 ,(2003) , 10.1214/LNMS/1215091155
Y. Li, L.-Q. Xu, J. Morphett, R. Jacobs, An integrated algorithm of incremental and robust PCA international conference on image processing. ,vol. 1, pp. 245- 248 ,(2003) , 10.1109/ICIP.2003.1246944
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
Yee Hwa Yang, Michael J Buckley, Sandrine Dudoit, Terence P Speed, Comparison of Methods for Image Analysis on cDNA Microarray Data Journal of Computational and Graphical Statistics. ,vol. 11, pp. 108- 136 ,(2002) , 10.1198/106186002317375640
David M. Rocke, Blythe Durbin, A model for measurement error for gene expression arrays. Journal of Computational Biology. ,vol. 8, pp. 557- 569 ,(2001) , 10.1089/106652701753307485
J. P. Brody, B. A. Williams, B. J. Wold, S. R. Quake, Significance and statistical errors in the analysis of DNA microarray data. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 99, pp. 12975- 12978 ,(2002) , 10.1073/PNAS.162468199
Charles Kooperberg, Thomas G. Fazzio, Jeffrey J. Delrow, Toshio Tsukiyama, Improved background correction for spotted DNA microarrays. Journal of Computational Biology. ,vol. 9, pp. 55- 66 ,(2002) , 10.1089/10665270252833190
Yee H. Yang, Sandrine Dudoit, Percy Luu, Terence P. Speed, Normalization for cDNA microarry data Microarrays : optical technologies and informatics. Conference. ,vol. 4266, pp. 141- 152 ,(2001) , 10.1117/12.427982
David J Duggan, Michael Bittner, Yidong Chen, Paul Meltzer, Jeffrey M. Trent, Expression profiling using cDNA microarrays Nature Genetics. ,vol. 21, pp. 10- 14 ,(1999) , 10.1038/4434