Exploration of distributional models for a novel intensity-dependent normalization procedure in censored gene expression data
Tài liệu tham khảo
Akaike, 1973, Information theory and an extension of the maximum likelihood principle, 267
Bioconductor, 2006. R package version 1.11.3, affydata: Affymetrix data for demonstration purpose
Bland, 1986, Statistical method for assessing agreement between two methods of clinical measurement, The Lancet, 307, 10.1016/S0140-6736(86)90837-8
Bland, 1999, Measuring agreement in method comparison studies, Statistical Methods in Medical Research, 8, 135, 10.1191/096228099673819272
Bolstad, 2003, A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19, 185, 10.1093/bioinformatics/19.2.185
Chen, 1997, Ratio-based decisions and the quantitative analysis of CDNA microarray images, Journal of Biomedical Optics, 2, 364, 10.1117/12.281504
Cleveland, 1988, Locally weighted regression: An approach to regression analysis by local fitting, Journal of the American Statistical Association, 83, 596, 10.2307/2289282
Cui, 2003, Transformations for CDNA microarray data, Statistical Applications in Genetics and Molecular Biology, 2, 10.2202/1544-6115.1009
Dabney, 2005, A new approach to intensity-dependent normalization of two-channel microarrays
D’Agostino, 1986
deBoor, 1978
Dudoit, 2002, Statistical methods for identifying differentially expressed genes in replicated CDNA microarray experiments, Statistica Sinica, 12, 111
Dudoit, 2003, Bioconductor R packages for exploratory analysis and normalization of CDNA microarray data, 73
Dunn, 1996, Randomized quantile residuals, Journal of Computational and Graphical Statistics, 236, 10.2307/1390802
Durbin, 2003, Estimation of transformation parameters for microarray data, Bioinformatics, 19, 1360, 10.1093/bioinformatics/btg178
Durbin, 2004, Variance-stabilizing transformations for two-color microarrays, Bioinformatics, 20, 660, 10.1093/bioinformatics/btg464
Ein-Dor, 2005, Outcome signature genes in breast cancer: is there a unique set?, Bioinformatics, 21, 171, 10.1093/bioinformatics/bth469
Futschik, 2004, Model selection and efficiency testing for normalisation of CDNA microarray data, Genome Biology, 5, R60, 10.1186/gb-2004-5-8-r60
Futschik, 2005, Olin: Optimized normalization, visualization and quality testing of two-channel microarray data, Bioinformatics Application Note, 21, 1724, 10.1093/bioinformatics/bti199
Hastie, 1992
Huber, 2002, Transcription profiling of renal cell carcinoma, Verhandlungen der Deutschen Gesellschaft für Pathologie, 86, 153
Huber, 2002, Variance stabilization applied to microarray data calibration and to the quantification of differential expression, Bioinformatics, 18 Suppl. 1, S96, 10.1093/bioinformatics/18.suppl_1.S96
Huber, 2002, Variance stabilization applied to microarray data calibration and to the quantification of differential expression, Bioinformatics, 18 Suppl 1, S96, 10.1093/bioinformatics/18.suppl_1.S96
Huber, 2003, Parameter estimation for the calibration and variance stabilization of microarray data, Statistical Applications in Genetics and Molecular Biology, 2, 1, 10.2202/1544-6115.1008
Huber, W., von Heydebreck, A., Vingron, M., 2004. Error Models for Microarray Intensities, Tech. Rep. 6, Bioconductor Project Working Papers. URL citeseer.ist.psu.edu/article/newton99differential.html
Ideker, 2000, Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data, Journal of Computational Biology, 7, 805, 10.1089/10665270050514945
Ioannidis, 2005, Microarrays and molecular research: Noise discovery?, Lancet, 365, 454, 10.1016/S0140-6736(05)17878-7
Kerr, 2001, Experimental design for gene expression microarrays, Biostatistics, 2, 183, 10.1093/biostatistics/2.2.183
Kerr, 2002, Sources of variation in microarray experiments
Khondoker, 2006, Statistical estimation of gene expression using multiple laser scans of microarrays, Bioinformatics, 22, 215, 10.1093/bioinformatics/bti790
Kotz, 1998
Lama, 2004, Some issues and perspectives in microarray data analysis in breast cancer: The need for an integrated research
Lee, 2004
Lee, 2004
Lemarechal, 1977, Bundle methods in nonsmooth optimization
Lindsey, 1999, A review of some extensions to generalized linear models, Statistics in Medicine, 18, 2223, 10.1002/(SICI)1097-0258(19990915/30)18:17/18<2223::AID-SIM251>3.0.CO;2-6
Luksan, 2001, Algorithm 811: Nda: Algorithms for nondifferentiable optimization, ACM Transactions on Mathematical Software, 27, 193, 10.1145/383738.383740
Mineo, 2005, A software tool for the exponential power distribution: The normalp package, j-J-STAT-SOFT, 12, 1
Pearson, 1962, The goodness-of-fit tests based on wn2 and un2, Biometrika, 49, 397, 10.2307/2333974
Pochet, 2004, Systematic benchmarking of microarray data classification: Assessing the role of non-linearity and dimensionality reduction, Bioinformatics, 20, 3185, 10.1093/bioinformatics/bth383
Puig, 2000, Tests of fit for the Laplace distribution, with applications, Technometrics, 42, 417, 10.2307/1270952
Purdom, 2005, Error distribution for gene expression data, Statistical Applications in Genetics and Molecular Biology, 4, 10.2202/1544-6115.1070
Qiu, 2005, The effects of normalization on the correlation structure of microarray data, BMC Bioinformatics, 6, 20, 10.1186/1471-2105-6-120
Quackenbush, 2002, Microarray data normalization and transformation, Nat Genet, 32 Suppl, 496, 10.1038/ng1032
R Development Core Team, 2004. R: A language and environment for statistical computing, R Foundation for Statistical Computing, Vienna, Austria, ISBN 3-900051-00-3, URL http://www.R-project.org
Rider, 1924, A generalized law of error, Journal of the American Statistical Association, 19, 217, 10.2307/2277233
Rocke, 2001, A model for measurement error for gene expression arrays, Journal of Computational Biology, 8, 557, 10.1089/106652701753307485
Russo, 2003, Advantages and limitations of microarray technology in human cancer, Oncogene, 22, 6497, 10.1038/sj.onc.1206865
Schwarz, 1978, Estimating the dimension of a model, Annals of Statistics, 6, 461, 10.1214/aos/1176344136
Sharov, 2004, The limits of log-ratios, BMC Biotechnology, 4
2003, Classification in microarray experiments, 93
Stephens, 1974, Edf statistics for goodness of fit and some comparisons, Journal of the American Statistical Association, 69, 730, 10.2307/2286009
Stephens, 1976, Asymptotic results for goodness-of-fit statistics with unknown parameters, Annals of Statistics, 4, 357, 10.1214/aos/1176343411
Strimmer, 2003, Modeling gene expression measurement error: A quasi-likelihood approach, BMC Bioinformatics, 4, 10, 10.1186/1471-2105-4-10
Tarca, 2005, A robust neural networks approach for spatial and intensity-dependent normalization of CDNA microarray data, Bioinformatics, 21, 2674, 10.1093/bioinformatics/bti397
Tibshirani, 2002, Pre-validation and inference in microarrays, Statistical Applications in Genetics and Molecular Biology, 1, 1, 10.2202/1544-6115.1000
van ’t Veer, 2002, Gene expression profiling predicts clinical outcome of breast cancer, Nature, 415, 530, 10.1038/415530a
Vianelli, 1963, La misura della variabilita condizionata in uno schema generale delle curve normali di frequenza, Statistica, 23, 447
Wit, 2003, Statistical adjustment of signal censoring in gene expression experiments, Bioinformatics, 19, 1055, 10.1093/bioinformatics/btg003
Wit, 2003
Workman, 2002, A new non-linear normalization method for reducing variability in DNA microarray experiments, Genome Biology, 3, 10.1186/gb-2002-3-9-research0048
Yang, 2002, Within the fold: Assessing differential expression measures and reproducibility in microarray assays, Genome Biology, 3
Yang, 2002, Normalization for CDNA microarray data: A robust composite method addressing single and multiple slide systematic variation, Nucleic Acids Research, 30, 10.1093/nar/30.4.e15
Yang, 2002, Design issues for CDNA microarray experiments, Nature Review Genetics, 3, 579, 10.1038/nrg863
Yeung, 2003, Multiclass classification of microarray data with repeated measurements: Application to cancer, Genome Biology, 4, R83, 10.1186/gb-2003-4-12-r83