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Supervised normalization of microarrays.

Mecham BH, Nelson PS, Storey JD.

Bioinformatics. 2010 May 15;26(10):1308-15. doi: 10.1093/bioinformatics/btq118. Epub 2010 Mar 31.


A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.

Bolstad BM, Irizarry RA, Astrand M, Speed TP.

Bioinformatics. 2003 Jan 22;19(2):185-93.


Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays.

Seo J, Bakay M, Chen YW, Hilmer S, Shneiderman B, Hoffman EP.

Bioinformatics. 2004 Nov 1;20(16):2534-44. Epub 2004 Apr 29.


Iterative rank-order normalization of gene expression microarray data.

Welsh EA, Eschrich SA, Berglund AE, Fenstermacher DA.

BMC Bioinformatics. 2013 May 7;14:153. doi: 10.1186/1471-2105-14-153.


Assessment of a novel multi-array normalization method based on spike-in control probes suitable for microRNA datasets with global decreases in expression.

Sewer A, Gubian S, Kogel U, Veljkovic E, Han W, Hengstermann A, Peitsch MC, Hoeng J.

BMC Res Notes. 2014 May 17;7:302. doi: 10.1186/1756-0500-7-302.


Analysis of boutique arrays: a universal method for the selection of the optimal data normalization procedure.

Uszczyńska B, Zyprych-Walczak J, Handschuh L, Szabelska A, Kaźmierczak M, Woronowicz W, Kozłowski P, Sikorski MM, Komarnicki M, Siatkowski I, Figlerowicz M.

Int J Mol Med. 2013 Sep;32(3):668-84. doi: 10.3892/ijmm.2013.1443. Epub 2013 Jul 15.


FABIA: factor analysis for bicluster acquisition.

Hochreiter S, Bodenhofer U, Heusel M, Mayr A, Mitterecker A, Kasim A, Khamiakova T, Van Sanden S, Lin D, Talloen W, Bijnens L, Göhlmann HW, Shkedy Z, Clevert DA.

Bioinformatics. 2010 Jun 15;26(12):1520-7. doi: 10.1093/bioinformatics/btq227. Epub 2010 Apr 23.


Spatial normalization of array-CGH data.

Neuvial P, Hupé P, Brito I, Liva S, Manié E, Brennetot C, Radvanyi F, Aurias A, Barillot E.

BMC Bioinformatics. 2006 May 22;7:264.


Can Zipf's law be adapted to normalize microarrays?

Lu T, Costello CM, Croucher PJ, Häsler R, Deuschl G, Schreiber S.

BMC Bioinformatics. 2005 Feb 23;6:37.


lumi: a pipeline for processing Illumina microarray.

Du P, Kibbe WA, Lin SM.

Bioinformatics. 2008 Jul 1;24(13):1547-8. doi: 10.1093/bioinformatics/btn224. Epub 2008 May 8.


A modified LOESS normalization applied to microRNA arrays: a comparative evaluation.

Risso D, Massa MS, Chiogna M, Romualdi C.

Bioinformatics. 2009 Oct 15;25(20):2685-91. doi: 10.1093/bioinformatics/btp443. Epub 2009 Jul 23.


Testing significance relative to a fold-change threshold is a TREAT.

McCarthy DJ, Smyth GK.

Bioinformatics. 2009 Mar 15;25(6):765-71. doi: 10.1093/bioinformatics/btp053. Epub 2009 Jan 28.


Importing ArrayExpress datasets into R/Bioconductor.

Kauffmann A, Rayner TF, Parkinson H, Kapushesky M, Lukk M, Brazma A, Huber W.

Bioinformatics. 2009 Aug 15;25(16):2092-4. doi: 10.1093/bioinformatics/btp354. Epub 2009 Jun 8.


Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis.

Wilson CL, Miller CJ.

Bioinformatics. 2005 Sep 15;21(18):3683-5. Epub 2005 Aug 2.


WebArray: an online platform for microarray data analysis.

Xia X, McClelland M, Wang Y.

BMC Bioinformatics. 2005 Dec 21;6:306.


A framework for oligonucleotide microarray preprocessing.

Carvalho BS, Irizarry RA.

Bioinformatics. 2010 Oct 1;26(19):2363-7. doi: 10.1093/bioinformatics/btq431. Epub 2010 Aug 5.


Transcript mapping with high-density oligonucleotide tiling arrays.

Huber W, Toedling J, Steinmetz LM.

Bioinformatics. 2006 Aug 15;22(16):1963-70. Epub 2006 Jun 20.


oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language.

Sanges R, Cordero F, Calogero RA.

Bioinformatics. 2007 Dec 15;23(24):3406-8. Epub 2007 Sep 17.

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