Publication

Kong SW, Hwang KB, Kim RD, Zhang BT, Greenberg SA, Kohane IS, Park PJ: CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays Bioinformatics 2005, 21: 2116-2117 [PubMed]

This site is an extended application of a method developed in the following paper, in which a comprehensive analysis is carried out for a HG-U95Av2 vs HG-U133A comparison.

Hwang KB, Kong SW, Greenberg SA, and Park PJ.(2004)
Combining gene expression data from different generations of oligonucleotide arrays. BMC Bioinformatics [PubMed]

Related papers

Affymetrix: User's guide to product comparison spreadsheets 2003, [http://www.affymetrix.com/support/technical/manual].

Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L, Kohane IS: Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 2002, 18:405-412.[PubMed]

Li J, Pankratz M, Johnson JA: Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays. Toxicol. Sci. 2002, 69:383-390.[PubMed]

Huminiecki L, Lloyd AT, Wolfe KH: Congruence of tissue expression profiles from Gene Expression Atlas, SAGEmap and TissueInfo databases. BMC Genomics 2003, 4:31.[PubMed]

Lee JK, Bussey KJ, Gwadry FG, Reinhold W, Riddick G, Pelletier SL, Nishizuka S, Szakacs G, Annereau JP, Shankavaram U, Lababidi S, Smith LH, Gottesman MM, Weinstein JN: Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cells. Genome Biology 2003, 4:R82.[PubMed]

Tan PK, Downey TJ, Jr ELS, Xu P, Fu D, Dimitrov DS, Lempicki RA, Raaka BM, Cam MC: Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res. 2003, 31:5676-5684.[PubMed]

Mah N, Thelin A, Lu T, Nikolaus S, Kuehbacher T, Gurbuz Y, Eickhoff H, Kloeppel G, Lehrach H, Mellgard B, Costello CM, Schreiber S: A comparison of oligonucleotide and cDNA-based microarray systems. Physiol. Genomics 2004,16:361-370.[PubMed]

Nimgaonkar A, Sanoudou D, Butte AJ, Haslett JN, Kunkel LM, Beggs AH, Kohane IS: Reproducibility of gene expression across generations of Affymetrix microarrays. BMC Bioinformatics 2003, 4:27.[PubMed]

Mecham BH, Wetmore DZ, Szallasi Z, Sadovsky Y, Kohane IS, Mariani TJ: Increased measurement accuracy for sequence-verified microarray probes. Physiol. Genomics 2004, 18:308-15.[PubMed]

Mecham BH, Klus GT, Strovel J, Augustus M, Byrne D, Bozso P, Wetmore DZ, Mariani TJ, Kohane IS, Szallasi Z: Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res. 2004, 32:e74.[PubMed]