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A weighted average difference method for detecting differentially expressed genes from microarray data.

Kadota K, Nakai Y, Shimizu K.

Algorithms Mol Biol. 2008 Jun 26;3:8.PMID: 18578891 [PubMed]Related articlesFree article

Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity.

Kadota K, Nakai Y, Shimizu K.

Algorithms Mol Biol. 2009 Apr 22;4:7.PMID: 19386098 [PubMed]Related articlesFree article

A unified framework for finding differentially expressed genes from microarray experiments.

Shaik JS, Yeasin M.

BMC Bioinformatics. 2007 Sep 18;8:347.PMID: 17877806 [PubMed - indexed for MEDLINE]Related articlesFree article

Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data.

Jeffery IB, Higgins DG, Culhane AC.

BMC Bioinformatics. 2006 Jul 26;7:359.PMID: 16872483 [PubMed - indexed for MEDLINE]Related articlesFree article

Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments.

Sartor MA, Tomlinson CR, Wesselkamper SC, Sivaganesan S, Leikauf GD, Medvedovic M.

BMC Bioinformatics. 2006 Dec 19;7:538.PMID: 17177995 [PubMed - indexed for MEDLINE]Related articlesFree article

A distribution free summarization method for Affymetrix GeneChip arrays.

Chen Z, McGee M, Liu Q, Scheuermann RH.

Bioinformatics. 2007 Feb 1;23(3):321-7. Epub 2006 Dec 5.PMID: 17148508 [PubMed - indexed for MEDLINE]Related articlesFree article

Methods for evaluating gene expression from Affymetrix microarray datasets.

Jiang N, Leach LJ, Hu X, Potokina E, Jia T, Druka A, Waugh R, Kearsey MJ, Luo ZW.

BMC Bioinformatics. 2008 Jun 17;9:284.PMID: 18559105 [PubMed - indexed for MEDLINE]Related articlesFree article

Reproducibility-optimized test statistic for ranking genes in microarray studies.

Elo LL, Filén S, Lahesmaa R, Aittokallio T.

IEEE/ACM Trans Comput Biol Bioinform. 2008 Jul-Sep;5(3):423-31.PMID: 18670045 [PubMed - indexed for MEDLINE]Related articles

The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies.

Shi L, Jones WD, Jensen RV, Harris SC, Perkins RG, Goodsaid FM, Guo L, Croner LJ, Boysen C, Fang H, Qian F, Amur S, Bao W, Barbacioru CC, Bertholet V, Cao XM, Chu TM, Collins PJ, Fan XH, Frueh FW, Fuscoe JC, Guo X, Han J, Herman D, Hong H, Kawasaki ES, Li QZ, Luo Y, Ma Y, Mei N, Peterson RL, Puri RK, Shippy R, Su Z, Sun YA, Sun H, Thorn B, Turpaz Y, Wang C, Wang SJ, Warrington JA, Willey JC, Wu J, Xie Q, Zhang L, Zhang L, Zhong S, Wolfinger RD, Tong W.

BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S10.PMID: 18793455 [PubMed - indexed for MEDLINE]Related articlesFree article

A new summarization method for Affymetrix probe level data.

Hochreiter S, Clevert DA, Obermayer K.

Bioinformatics. 2006 Apr 15;22(8):943-9. Epub 2006 Feb 10.PMID: 16473874 [PubMed - indexed for MEDLINE]Related articlesFree article

Support vector machine quantile regression for detecting differentially expressed genes in microarray analysis.

Sohn I, Kim S, Hwang C, Lee JW, Shim J.

Methods Inf Med. 2008;47(5):459-67.PMID: 18852921 [PubMed - indexed for MEDLINE]Related articles

Empirical validation of the S-Score algorithm in the analysis of gene expression data.

Kennedy RE, Archer KJ, Miles MF.

BMC Bioinformatics. 2006 Mar 17;7:154.PMID: 16545131 [PubMed - indexed for MEDLINE]Related articlesFree article

Very Important Pool (VIP) genes--an application for microarray-based molecular signatures.

Su Z, Hong H, Fang H, Shi L, Perkins R, Tong W.

BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S9.PMID: 18793473 [PubMed - indexed for MEDLINE]Related articlesFree article

Investigation of reproducibility of differentially expressed genes in DNA microarrays through statistical simulation.

Fan X, Shi L, Fang H, Harris S, Perkins R, Tong W.

BMC Proc. 2009 Mar 10;3 Suppl 2:S4.PMID: 19278560 [PubMed]Related articlesFree article

Probability fold change: a robust computational approach for identifying differentially expressed gene lists.

Deng X, Xu J, Hui J, Wang C.

Comput Methods Programs Biomed. 2009 Feb;93(2):124-39. Epub 2008 Oct 7.PMID: 18842321 [PubMed - indexed for MEDLINE]Related articles

Fisher's combined p-value for detecting differentially expressed genes using Affymetrix expression arrays.

Hess A, Iyer H.

BMC Genomics. 2007 Apr 9;8:96.PMID: 17419876 [PubMed - indexed for MEDLINE]Related articlesFree article

BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets.

Alston MJ, Seers J, Hinton JC, Lucchini S.

BMC Bioinformatics. 2010 Feb 3;11:73.PMID: 20128918 [PubMed - in process]Related articlesFree article

Empirical Bayes models for multiple probe type microarrays at the probe level.

Astrand M, Mostad P, Rudemo M.

BMC Bioinformatics. 2008 Mar 20;9:156.PMID: 18366694 [PubMed - indexed for MEDLINE]Related articlesFree article

Selection of differentially expressed genes in microarray data analysis.

Chen JJ, Wang SJ, Tsai CA, Lin CJ.

Pharmacogenomics J. 2007 Jun;7(3):212-20. Epub 2006 Aug 29.PMID: 16940966 [PubMed - indexed for MEDLINE]Related articles

A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments.

Hong F, Breitling R.

Bioinformatics. 2008 Feb 1;24(3):374-82. Epub 2008 Jan 18.PMID: 18204063 [PubMed - indexed for MEDLINE]Related articlesFree article