TY - JOUR AU - Bolstad, B. M. AU - Irizarry, R. A. AU - Astrand, M. AU - Speed, T. P. PY - 2003 DA - 2003// TI - A comparison of normalization methods for high density oligonucleotide array data based on variance and bias JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/19.2.185 DO - 10.1093/bioinformatics/19.2.185 ID - Bolstad2003 ER - TY - JOUR AU - Cleveland, W. S. PY - 1981 DA - 1981// TI - Lowess - a Program for Smoothing Scatterplots by Robust Locally Weighted Regression JO - American Statistician VL - 35 UR - https://doi.org/10.2307/2683591 DO - 10.2307/2683591 ID - Cleveland1981 ER - TY - JOUR AU - Dudoit, S. AU - Yang, Y. H. AU - Callow, M. J. AU - Speed, T. P. PY - 2002 DA - 2002// TI - Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments JO - Statistica Sinica VL - 12 ID - Dudoit2002 ER - TY - JOUR AU - Choe, S. E. AU - Boutros, M. AU - Michelson, A. M. AU - Church, G. M. AU - Halfon, M. S. PY - 2005 DA - 2005// TI - Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset JO - Genome Biol VL - 6 UR - https://doi.org/10.1186/gb-2005-6-2-r16 DO - 10.1186/gb-2005-6-2-r16 ID - Choe2005 ER - TY - JOUR AU - Pelz, C. R. AU - Kulesz-Martin, M. AU - Bagby, G. AU - Sears, R. C. PY - 2008 DA - 2008// TI - Global rank-invariant set normalization (GRSN) to reduce systematic distortions in microarray data JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-520 DO - 10.1186/1471-2105-9-520 ID - Pelz2008 ER - TY - JOUR AU - Lu, Y. AU - Huggins, P. AU - Bar-Joseph, Z. PY - 2009 DA - 2009// TI - Cross species analysis of microarray expression data JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp247 DO - 10.1093/bioinformatics/btp247 ID - Lu2009 ER - TY - JOUR AU - Oshlack, A. AU - Chabot, A. E. AU - Smyth, G. K. AU - Gilad, Y. PY - 2007 DA - 2007// TI - Using DNA microarrays to study gene expression in closely related species JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm111 DO - 10.1093/bioinformatics/btm111 ID - Oshlack2007 ER - TY - JOUR AU - Gresham, D. AU - Ruderfer, D. M. AU - Pratt, S. C. AU - Schacherer, J. AU - Dunham, M. J. AU - Botstein, D. AU - Kruglyak, L. PY - 2006 DA - 2006// TI - Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray JO - Science VL - 311 UR - https://doi.org/10.1126/science.1123726 DO - 10.1126/science.1123726 ID - Gresham2006 ER - TY - JOUR AU - Oshlack, A. AU - Emslie, D. AU - Corcoran, L. M. AU - Smyth, G. K. PY - 2007 DA - 2007// TI - Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes JO - Genome Biol VL - 8 UR - https://doi.org/10.1186/gb-2007-8-1-r2 DO - 10.1186/gb-2007-8-1-r2 ID - Oshlack2007 ER - TY - JOUR AU - Li, C. AU - Wong, W. PY - 2001 DA - 2001// TI - Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application JO - Genome Biology VL - 2 ID - Li2001 ER - TY - JOUR AU - Savonet, V. AU - Maenhaut, C. AU - Miot, F. AU - Pirson, I. PY - 1997 DA - 1997// TI - Pitfalls in the use of several ''housekeeping'' genes as standards for quantitation of mRNA: The example of thyroid cells JO - Analytical Biochemistry VL - 247 UR - https://doi.org/10.1006/abio.1997.2055 DO - 10.1006/abio.1997.2055 ID - Savonet1997 ER - TY - JOUR AU - Khimani, A. H. AU - Mhashilkar, A. M. AU - Mikulskis, A. AU - O'Malley, M. AU - Liao, J. AU - Golenko, E. E. AU - Mayer, P. AU - Chada, S. AU - Killian, J. B. AU - Lott, S. T. PY - 2005 DA - 2005// TI - Housekeeping genes in cancer: normalization of array data JO - Biotechniques VL - 38 UR - https://doi.org/10.2144/05385ST04 DO - 10.2144/05385ST04 ID - Khimani2005 ER - TY - JOUR AU - Steele, B. K. AU - Meyers, C. AU - Ozbun, M. A. PY - 2002 DA - 2002// TI - Variable expression of some "housekeeping" genes during human keratinocyte differentiation JO - Analytical Biochemistry VL - 307 UR - https://doi.org/10.1016/S0003-2697(02)00045-3 DO - 10.1016/S0003-2697(02)00045-3 ID - Steele2002 ER - TY - JOUR AU - Waxman, S. AU - Wurmbach, E. PY - 2007 DA - 2007// TI - De-regulation of common housekeeping genes in hepatocellular carcinoma JO - BMC Genomics VL - 8 UR - https://doi.org/10.1186/1471-2164-8-243 DO - 10.1186/1471-2164-8-243 ID - Waxman2007 ER - TY - STD TI - Ni TT, Lemon WJ, Shyr Y, Zhong TP: use of normalization methods for analysis of microarrays containing a high degree of gene effects. BMC Bioinformatics 2008., 9(505): ID - ref15 ER - TY - JOUR AU - Irizarry, R. A. AU - Cope, L. M. AU - Wu, Z. J. PY - 2006 DA - 2006// TI - Feature-level exploration of a published Affymetrix GeneChip control dataset JO - Genome Biology VL - 7 UR - https://doi.org/10.1186/gb-2006-7-8-404 DO - 10.1186/gb-2006-7-8-404 ID - Irizarry2006 ER - TY - STD TI - Choe SE, Boutros M, Michelson AM, Church GM, Halfon MS: Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biology 2005., 6(2): ID - ref17 ER - TY - STD TI - Dabney AR, Storey JD: A reanalysis of a published Affymetrix GeneChip control dataset. Genome Biology 2006., 7(3): ID - ref18 ER - TY - JOUR AU - Gaile, D. P. AU - Miecznikowski, J. C. PY - 2007 DA - 2007// TI - Putative null distributions corresponding to tests of differential expression in the Golden Spike dataset are intensity dependent JO - BMC Genomics VL - 8 UR - https://doi.org/10.1186/1471-2164-8-105 DO - 10.1186/1471-2164-8-105 ID - Gaile2007 ER - TY - JOUR AU - Pearson, R. D. PY - 2008 DA - 2008// TI - A comprehensive re-analysis of the Golden Spike data: towards a benchmark for differential expression methods JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-164 DO - 10.1186/1471-2105-9-164 ID - Pearson2008 ER - TY - CHAP AU - Pearson, R. D. PY - 2008 DA - 2008// TI - A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods BT - BMC Bioinformatics ID - Pearson2008 ER - TY - STD TI - Gadbury GL, Xiang QF, Yang L, Barnes S, Page GP, Allison DB: Evaluating Statistical Methods Using Plasmode Data Sets in the Age of Massive Public Databases: An Illustration Using False Discovery Rates. Plos Genetics 2008., 4(6): ID - ref22 ER - TY - JOUR AU - Durig, J. AU - Bug, S. AU - Klein-Hitpass, L. AU - Boes, T. AU - Jons, T. AU - Martin-Subero, J. I. AU - Harder, L. AU - Baudis, M. AU - Duhrsen, U. AU - Siebert, R. PY - 2007 DA - 2007// TI - Combined single nucleotide polymorphism-based genomic mapping and global gene expression profiling identifies novel chromosomal imbalances, mechanisms and candidate genes important in the pathogenesis of T-cell prolymphocytic leukemia with inv(14)(q11q32) JO - Leukemia VL - 21 UR - https://doi.org/10.1038/sj.leu.2404877 DO - 10.1038/sj.leu.2404877 ID - Durig2007 ER - TY - JOUR AU - Irizarry, R. A. AU - Hobbs, B. AU - Collin, F. AU - Beazer-Barclay, Y. D. AU - Antonellis, K. J. AU - Scherf, U. AU - Speed, T. P. PY - 2003 DA - 2003// TI - Exploration, normalization, and summaries of high density oligonucleotide array probe level data JO - Biostatistics VL - 4 UR - https://doi.org/10.1093/biostatistics/4.2.249 DO - 10.1093/biostatistics/4.2.249 ID - Irizarry2003 ER - TY - JOUR AU - Hochreiter, S. AU - Clevert, D. A. AU - Obermayer, K. PY - 2006 DA - 2006// TI - A new summarization method for affymetrix probe level data JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl033 DO - 10.1093/bioinformatics/btl033 ID - Hochreiter2006 ER - TY - CHAP AU - Opgen-Rhein, R. AU - Strimmer, K. PY - 2007 DA - 2007// TI - Accurate ranking of differentially expressed genes by a distribution-free shrinkage approach BT - Statistical Applications in Genetics and Molecular Biology ID - Opgen-Rhein2007 ER - TY - JOUR AU - Sartor, M. A. AU - Tomlinson, C. R. AU - Wesselkamper, S. C. AU - Sivaganesan, S. AU - Leikauf, G. D. AU - Medvedovic, M. PY - 2006 DA - 2006// TI - Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-538 DO - 10.1186/1471-2105-7-538 ID - Sartor2006 ER -