Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity
暂无分享,去创建一个
[1] Pierre Baldi,et al. A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes , 2001, Bioinform..
[2] R. Tibshirani,et al. Significance analysis of microarrays applied to the ionizing radiation response , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[3] C. Li,et al. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[4] Martin Vingron,et al. Variance stabilization applied to microarray data calibration and to the quantification of differential expression , 2002, ISMB.
[5] Wei-Min Liu,et al. Robust estimators for expression analysis , 2002, Bioinform..
[6] Rafael A Irizarry,et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. , 2003, Biostatistics.
[7] Rainer Breitling,et al. Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments , 2004, FEBS letters.
[8] Benjamin M. Bolstad,et al. affy - analysis of Affymetrix GeneChip data at the probe level , 2004, Bioinform..
[9] Rafael A. Irizarry,et al. A Model-Based Background Adjustment for Oligonucleotide Expression Arrays , 2004 .
[10] G. Church,et al. Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset , 2005, Genome Biology.
[11] Gordon K Smyth,et al. Statistical Applications in Genetics and Molecular Biology Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2011 .
[12] Jean YH Yang,et al. Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.
[13] Neil D. Lawrence,et al. A tractable probabilistic model for Affymetrix probe-level analysis across multiple chips , 2005, Bioinform..
[14] Sébastien Lemieux,et al. Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression , 2006, BMC Bioinformatics.
[15] Hanlee P. Ji,et al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. , 2006, Nature biotechnology.
[16] Rainer Breitling,et al. RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis , 2006, Bioinform..
[17] Klaus Obermayer,et al. A new summarization method for affymetrix probe level data , 2006, Bioinform..
[18] Maqc Consortium. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements , 2006, Nature Biotechnology.
[19] Neil D. Lawrence,et al. Probe-level measurement error improves accuracy in detecting differential gene expression , 2006, Bioinform..
[20] Rafael A. Irizarry,et al. Comparison of Affymetrix GeneChip expression measures , 2006, Bioinform..
[21] Mario Medvedovic,et al. Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments , 2006, BMC Bioinformatics.
[22] Koji Kadota,et al. GOGOT: a method for the identification of differentially expressed fragments from cDNA-AFLP data , 2007, Algorithms for Molecular Biology.
[23] Qingzhong Liu,et al. A distribution free summarization method for Affymetrix GeneChip arrays. , 2007, Bioinformatics.
[24] Koji Kadota,et al. A weighted average difference method for detecting differentially expressed genes from microarray data , 2008, Algorithms for Molecular Biology.
[25] Chao Cheng,et al. A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays , 2007, BMC Bioinformatics.
[26] Richard D. Pearson,et al. A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods , 2008, BMC Bioinformatics.
[27] Dennis B. Troup,et al. NCBI GEO: mining tens of millions of expression profiles—database and tools update , 2006, Nucleic Acids Res..
[28] Korbinian Strimmer,et al. Statistical Applications in Genetics and Molecular Biology , 2005 .
[29] Koji Kadota,et al. Up-Regulation of Genes Related to the Ubiquitin-Proteasome System in the Brown Adipose Tissue of 24-h-Fasted Rats , 2008, Bioscience, biotechnology, and biochemistry.
[30] Stephan Preibisch,et al. "Hook"-calibration of GeneChip-microarrays: Chip characteristics and expression measures , 2008, Algorithms for Molecular Biology.
[31] Catalin C. Barbacioru,et al. The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies , 2008, BMC Bioinformatics.
[32] Jin Xu,et al. Robustified MANOVA with applications in detecting differentially expressed genes from oligonucleotide arrays , 2008, Bioinform..
[33] Stephan Preibisch,et al. "Hook"-calibration of GeneChip-microarrays: Theory and algorithm , 2008, Algorithms for Molecular Biology.