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1:

Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis.

Hoffmann R, Seidl T, Dugas M.

Genome Biol. 2002 Jun 14;3(7):RESEARCH0033. Epub 2002 Jun 14.

PMID: 12184807 [PubMed - indexed for MEDLINE]

2:

Effect of various normalization methods on Applied Biosystems expression array system data.

Barbacioru CC, Wang Y, Canales RD, Sun YA, Keys DN, Chan F, Poulter KA, Samaha RR.

BMC Bioinformatics. 2006 Dec 15;7:533.

PMID: 17173684 [PubMed - indexed for MEDLINE]

3:

An associative analysis of gene expression array data.

Dozmorov I, Centola M.

Bioinformatics. 2003 Jan 22;19(2):204-11.

PMID: 12538240 [PubMed - indexed for MEDLINE]

4:

The statistics of identifying differentially expressed genes in Expresso and TM4: a comparison.

Sioson AA, Mane SP, Li P, Sha W, Heath LS, Bohnert HJ, Grene R.

BMC Bioinformatics. 2006 Apr 20;7:215.

PMID: 16626497 [PubMed - indexed for MEDLINE]

5:

Finding differentially expressed genes in two-channel DNA microarray datasets: how to increase reliability of data preprocessing.

Rotter A, Hren M, Baebler S, Blejec A, Gruden K.

OMICS. 2008 Sep;12(3):171-82.

PMID: 18771401 [PubMed - indexed for MEDLINE]

6:

The effects of normalization on the correlation structure of microarray data.

Qiu X, Brooks AI, Klebanov L, Yakovlev N.

BMC Bioinformatics. 2005 May 16;6:120.

PMID: 15904488 [PubMed - indexed for MEDLINE]

7:

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]

8:

Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data.

Shedden K, Chen W, Kuick R, Ghosh D, Macdonald J, Cho KR, Giordano TJ, Gruber SB, Fearon ER, Taylor JM, Hanash S.

BMC Bioinformatics. 2005 Feb 10;6:26.

PMID: 15705192 [PubMed - indexed for MEDLINE]

9:

Identifying differentially expressed genes using false discovery rate controlling procedures.

Reiner A, Yekutieli D, Benjamini Y.

Bioinformatics. 2003 Feb 12;19(3):368-75.

PMID: 12584122 [PubMed - indexed for MEDLINE]

10:

Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes.

Oshlack A, Emslie D, Corcoran LM, Smyth GK.

Genome Biol. 2007;8(1):R2.

PMID: 17204140 [PubMed - indexed for MEDLINE]

11:

Cross platform microarray analysis for robust identification of differentially expressed genes.

Bosotti R, Locatelli G, Healy S, Scacheri E, Sartori L, Mercurio C, Calogero R, Isacchi A.

BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S5.

PMID: 17430572 [PubMed - indexed for MEDLINE]

12:

A comparative analysis of data generated using two different target preparation methods for hybridization to high-density oligonucleotide microarrays.

Gold D, Coombes K, Medhane D, Ramaswamy A, Ju Z, Strong L, Koo JS, Kapoor M.

BMC Genomics. 2004 Jan 6;5(1):2.

PMID: 14709180 [PubMed - indexed for MEDLINE]

14:

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]

15:

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]

16:

Selecting normalization genes for small diagnostic microarrays.

Jaeger J, Spang R.

BMC Bioinformatics. 2006 Aug 22;7:388.

PMID: 16925821 [PubMed - indexed for MEDLINE]

17:

Sample size for detecting differentially expressed genes in microarray experiments.

Wei C, Li J, Bumgarner RE.

BMC Genomics. 2004 Nov 8;5(1):87.

PMID: 15533245 [PubMed - indexed for MEDLINE]

18:

Normalization and quantification of differential expression in gene expression microarrays.

Steinhoff C, Vingron M.

Brief Bioinform. 2006 Jun;7(2):166-77. Epub 2006 Mar 7. Review.

PMID: 16772260 [PubMed - indexed for MEDLINE]

19:

Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons.

Harr B, Schlötterer C.

Nucleic Acids Res. 2006 Jan 23;34(2):e8.

PMID: 16432259 [PubMed - indexed for MEDLINE]

20:

Normal uniform mixture differential gene expression detection for cDNA microarrays.

Dean N, Raftery AE.

BMC Bioinformatics. 2005 Jul 12;6:173.

PMID: 16011807 [PubMed - indexed for MEDLINE]

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