PubMed

On the necessity of different statistical treatment for Illumina BeadChip and Affymetrix GeneChip data and its significance for biological interpretation.

Wong WC, Loh M, Eisenhaber F.

Biol Direct. 2008 Jun 3;3:23.PMID: 18522715 [PubMed - indexed for MEDLINE]Related articlesFree article

The chemiluminescence based Ziplex automated workstation focus array reproduces ovarian cancer Affymetrix GeneChip expression profiles.

Quinn MC, Wilson DJ, Young F, Dempsey AA, Arcand SL, Birch AH, Wojnarowicz PM, Provencher D, Mes-Masson AM, Englert D, Tonin PN.

J Transl Med. 2009 Jul 6;7:55.PMID: 19580657 [PubMed - indexed for MEDLINE]Related articlesFree article

Statistical analysis of high-density oligonucleotide arrays: a multiplicative noise model.

Sásik R, Calvo E, Corbeil J.

Bioinformatics. 2002 Dec;18(12):1633-40.PMID: 12490448 [PubMed - indexed for MEDLINE]Related articlesFree article

Importance of randomization in microarray experimental designs with Illumina platforms.

Verdugo RA, Deschepper CF, Muñoz G, Pomp D, Churchill GA.

Nucleic Acids Res. 2009 Sep;37(17):5610-8. Epub 2009 Jul 17.PMID: 19617374 [PubMed - indexed for MEDLINE]Related articlesFree article

Relative power and sample size analysis on gene expression profiling data.

van Iterson M, 't Hoen PA, Pedotti P, Hooiveld GJ, den Dunnen JT, van Ommen GJ, Boer JM, Menezes RX.

BMC Genomics. 2009 Sep 17;10:439.PMID: 19758461 [PubMed - indexed for MEDLINE]Related articlesFree article

A statistical method for predicting splice variants between two groups of samples using GeneChip expression array data.

Fan W, Khalid N, Hallahan AR, Olson JM, Zhao LP.

Theor Biol Med Model. 2006 Apr 7;3:19.PMID: 16603076 [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

Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells.

Maouche S, Poirier O, Godefroy T, Olaso R, Gut I, Collet JP, Montalescot G, Cambien F.

BMC Genomics. 2008 Jun 25;9:302.PMID: 18578872 [PubMed - indexed for MEDLINE]Related articlesFree article

Putative null distributions corresponding to tests of differential expression in the Golden Spike dataset are intensity dependent.

Gaile DP, Miecznikowski JC.

BMC Genomics. 2007 Apr 19;8:105.PMID: 17445265 [PubMed - indexed for MEDLINE]Related articlesFree article

Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms.

Barnes M, Freudenberg J, Thompson S, Aronow B, Pavlidis P.

Nucleic Acids Res. 2005 Oct 19;33(18):5914-23. Print 2005.PMID: 16237126 [PubMed - indexed for MEDLINE]Related articlesFree article

A rapid method for microarray cross platform comparisons using gene expression signatures.

Cheadle C, Becker KG, Cho-Chung YS, Nesterova M, Watkins T, Wood W 3rd, Prabhu V, Barnes KC.

Mol Cell Probes. 2007 Feb;21(1):35-46. Epub 2006 Aug 10.PMID: 16982174 [PubMed - indexed for MEDLINE]Related articles

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

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]Related articlesFree article

Can subtle changes in gene expression be consistently detected with different microarray platforms?

Pedotti P, 't Hoen PA, Vreugdenhil E, Schenk GJ, Vossen RH, Ariyurek Y, de Hollander M, Kuiper R, van Ommen GJ, den Dunnen JT, Boer JM, de Menezes RX.

BMC Genomics. 2008 Mar 10;9:124.PMID: 18331641 [PubMed - indexed for MEDLINE]Related articlesFree article

Expression profiling of human renal carcinomas with functional taxonomic analysis.

Gieseg MA, Cody T, Man MZ, Madore SJ, Rubin MA, Kaldjian EP.

BMC Bioinformatics. 2002 Sep 30;3:26.PMID: 12356337 [PubMed - indexed for MEDLINE]Related articlesFree article

Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors.

Baumbusch LO, Aarøe J, Johansen FE, Hicks J, Sun H, Bruhn L, Gunderson K, Naume B, Kristensen VN, Liestøl K, Børresen-Dale AL, Lingjaerde OC.

BMC Genomics. 2008 Aug 8;9:379.PMID: 18691401 [PubMed - indexed for MEDLINE]Related articlesFree article

Illumina WG-6 BeadChip strips should be normalized separately.

Shi W, Banerjee A, Ritchie ME, Gerondakis S, Smyth GK.

BMC Bioinformatics. 2009 Nov 11;10:372.PMID: 19903361 [PubMed - indexed for MEDLINE]Related articlesFree article

Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations.

Shippy R, Sendera TJ, Lockner R, Palaniappan C, Kaysser-Kranich T, Watts G, Alsobrook J.

BMC Genomics. 2004 Sep 2;5(1):61.PMID: 15345031 [PubMed - indexed for MEDLINE]Related articlesFree article

A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms.

Woo Y, Affourtit J, Daigle S, Viale A, Johnson K, Naggert J, Churchill G.

J Biomol Tech. 2004 Dec;15(4):276-84.PMID: 15585824 [PubMed - indexed for MEDLINE]Related articlesFree article

SiPaGene: A new repository for instant online retrieval, sharing and meta-analyses of GeneChip expression data.

Menssen A, Edinger G, Grün JR, Haase U, Baumgrass R, Grützkau A, Radbruch A, Burmester GR, Häupl T.

BMC Genomics. 2009 Mar 5;10:98.PMID: 19265543 [PubMed - indexed for MEDLINE]Related articlesFree article