Optimized LOWESS normalization parameter selection for DNA microarray data

Schena M, Shalon D, Davis RW, Brown PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270: 467–470.

Goryachev AB, MacGregor PF, Edwards AM: Unfolding of microarray data. Journal of Computational Biology 2001, 8: 443–461. 10.1089/106652701752236232

Ideker T, Thorsson V, Siegel AF, Hood LE: Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data. Journal of Computational Biology 2000, 7: 805–817. 10.1089/10665270050514945

Kerr MK, Martin M, Churchill GA: Analysis of variance for gene expression microarray data. Journal of Computational Biology 2000, 7: 819–837. 10.1089/10665270050514954

Tseng GC, Oh MK, Rohlin L, Liao JC, Wong WH: Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Research 2001, 29: 2549–2557. 10.1093/nar/29.12.2549

Wang X, Ghosh S, Guo SW: Quantitative quality control in microarray image processing and data acquisition. Nucleic Acids Research 2001, 19: e75. 10.1093/nar/29.15.e75

Dobbin K, Shih JH, Simon R: Statisical design of reverse dye microarrays. Bioinformatics 2003, 19: 803–810. 10.1093/bioinformatics/btg076

Cleveland WS: Robust locally weighted regression and smoothing scatterplots. Journal of the American Statistical Association 1979, 74: 829–836.

Ihaka R, Gentleman R: R: a language for data analysis and graphics. Journal of Computational and Graphical Statistics 1996, 5: 299–314.

Engelen K, Coessens B, Marchal K, Moor BD: MARAN: normalizing micro-array data. Bioinformatics 2003, 19: 893–894. 10.1093/bioinformatics/btg085

Venet D: MatArray: a Matlab toolbox for microarray data. Bioinformatics 2003, 19: 659–660. 10.1093/bioinformatics/btg046

Quackenbush J: Microarray data normalization and transformation. Nature Genetics 2002, Suppl 32: 496–501. 10.1038/ng1032

Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research 2002, 30: e15. 10.1093/nar/30.4.e15

Cleveland WS, Devlin SJ: Locally weighted regression: an approach to regression analysis by local fitting. Journal of the American Statistical Association 1988, 83: 596–610.

Dudoit S, Yang YH, Callow MJ, Speed TP: Statistical methods for identifying genes with differential expression in replicated cDNA microarray experiments. Statistical Sinica 2002, 12: 111–139.

Yang YH, Dudoit S, Luu P, Speed TP: Normalization for cDNA microarray data. In In Microarrays: optical technologies and informatics. Volume 4266. Edited by: Bittner M, Chen Y, Dorsel A, Dougherty ER. San Jose, CA, USA: SPIE; 2001:141–152.

Bolstad BM, Irizarry RA, Åstrand M, Speed TP: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19: 185–193. 10.1093/bioinformatics/19.2.185

Edwards D: Non-linear normalization and background correction in one-channel cDNA microarray studies. Bioinformatics 2003, 19: 825–833. 10.1093/bioinformatics/btg083

Wilson DL, Buckley MJ, Helliwell CA, Wilson IW: New normalization methods for cDNA microarray data. Bioinformatics 2003, 19: 1325–1332. 10.1093/bioinformatics/btg146

Järvinen AK, Hautaniemi S, Edgren H, Auvinen P, Saarela J, Kallioniemi OP, Monni O: Are data from different gene expression microarray platforms comparable? Genomics 2004, 84: 1164–1168. 10.1016/j.ygeno.2004.01.004

Supplementary Webpage (Self vs. Self data)[http://www.ece.ucsb.edu/pubs/bmc/]

Supplementary Webpage (Breast Cancer data)[http://sigwww.cs.tut.fi/TICSP/Jarvinen_et_al_2003/]

Dobbin K, Shih JH, Simon R: Questions and answers on design of dual-label microarrays for identifying differentially expressed genes. J Nat Cancer Inst 2003, 95: 1362–1369.

Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM: Expression profiling using cDNA microarrays. Nature Genetics 1999, 21: 10–14. 10.1038/4434

Finkelstein D, Ewing R, Gollub J, Sterky F, Cherry JM, Somerville S: Microarray data quality analysis: lessons from the AFGC project. Plant Molecular Biology 2002, 48: 119–131. 10.1023/A:1013765922672

Holloway AJ, van Laar RK, Tothill RW, Bowtell DDL: Options available – from start to finish – for obtaining data from DNA microarrays II. Nature Genetics 2002, 32: 481–489. 10.1038/ng1030

Fan J, Gijbels I: Local Polynomial Modelling and its Applications. London: Chapman and Hall; 1996.

Forsythe GE, Malcolm MA, Moler CB: Computer Methods for Mathematical Computations. Englewood Cliffs, NJ: Prentice-Hall, Inc; 1977.

Chen Y, Kamat V, Dougherty ER, Bittner ML, Meltzer PS, Trent JM: Ratio statistics of gene expression levels and applications to microarray data analysis. Bioinformatics 2002, 18: 1207–1215. 10.1093/bioinformatics/18.9.1207

Hautaniemi S, Edgren H, Vesanen P, Wolf M, Järvinen AK, Yli-Harja O, Astola J, Kallioniemi O, Monni O: A Novel Strategy for Microarray Quality Control Using Bayesian Networks. Bioinformatics 2003, 19: 2031–2038. 10.1093/bioinformatics/btg275

Lee M, Kuo F, Whitmore G, Sklar J: Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl Acad Sci USA 2000, 97: 9834–9839. 10.1073/pnas.97.18.9834

Yang YH, Speed TP: Design issues for cDNA microarray experiments. Nature Reviews Genetics 2002, 3: 579–588.

Eilers PHC, Goeman JJ: Enhancing scatterplots with smoothed densities. Bioinformatics 2004, 20: 623–628. 10.1093/bioinformatics/btg454

Bevington PR, Robinson DK: Data Reduction and Error Analysis for the Physical Sciences. 2nd edition. Boston, MA: WCB/McGraw-Hill; 1992.

Hyman E, Kauraniemi P, Hautaniemi S, Wolf M, Mousses S, Rozenblum E, Ringnér M, Sauter G, Monni O, Elkahloun A, Kallioniemi OP, Kallioniemi A: Impact of DNA amplification on gene expression patterns in breast cancer. Cancer Research 2002, 62: 6240–6245.

Clark J, Edwards S, Feber A, Flohr P, John M, Giddings I, Crossland S, Stratton MR, Wooster R, Campbell C, Cooper CS: Genome-wide screening for complete genetic loss in prostate cancer by comparative hybridization onto cDNA microarrays. Oncogene 2003, 22: 1247–1252. 10.1038/sj.onc.1206247

Borkowf CB, Albert PS, Abnet CC: Using lowess to remove systematic trends over time in predictor variables prior to logistic regression with quantile categories. Statistics in Medicine 2003, 22: 1477–1493. 10.1002/sim.1507

Mazerolle M: Detrimental effects of peat mining on amphibian abundance and species richness in bogs. Biological Conservation 2003, 113: 215–223. 10.1016/S0006-3207(02)00360-9

Hen I, Sakov A, Kafkafi N, Golani I, Benjamini Y: The dynamics of spatial behavior: how can robust smoothing techniques help? Journal of Neuroscience Methods 2004, 133: 161–172. 10.1016/j.jneumeth.2003.10.013

Monni O, Bärlund M, Mousses S, Kononen J, Sauter G, Heiskanen M, Paavola P, Avela K, Chen Y, Bittner M, Kallioniemi A: Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer. Proc Natl Acad Sci 2001, 98: 5711–5716. 10.1073/pnas.091582298