Thu, 21 Aug 2008 14:58:17 BST CiteULike: hpiwowar's Quackenbush http://www.citeulike.org/user/hpiwowar/author/Quackenbush CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/hpiwowar/article/2784212 <i>Science (New York, N.Y.), Vol. 298, No. 5593. (18 October 2002)</i> Standards for microarray data. CA Ball G Sherlock H Parkinson P Rocca-Sera C Brooksbank HC Causton D Cavalieri T Gaasterland P Hingamp F Holstege M Ringwald P Spellman CJ Stoeckert JE Stewart R Taylor A Brazma J Quackenbush Science (New York, N.Y.), Vol. 298, No. 5593. (18 October 2002) 2008-05-11T11:46:56-00:00 2002 Science (New York, N.Y.) 1095-9203 298 5593 all data-reuse data-sharing letter microarray standards http://www.citeulike.org/user/hpiwowar/article/1976462 <i>PLoS Biol, Vol. 2, No. 9. (September 2004)</i> Submission of microarray data to public repositories. CA Ball A Brazma H Causton S Chervitz R Edgar P Hingamp JC Matese H Parkinson J Quackenbush M Ringwald SA Sansone G Sherlock P Spellman C Stoeckert Y Tateno R Taylor J White N Winegarden doi:10.1371/journal.pbio.0020317 PLoS Biol, Vol. 2, No. 9. (September 2004) 2007-11-24T23:41:54-00:00 2004 PLoS Biol 1545-7885 2 9 all arrayexpress databases data-sharing elpub geo history important microarrays policies publication http://www.citeulike.org/user/hpiwowar/article/518652 <i>Nat Methods, Vol. 2, No. 5. (2005), pp. 345-50.</i><br /><br />Microarray technology is a powerful tool for measuring RNA expression for thousands of genes at once. Various studies have been published comparing competing platforms with mixed results: some find agreement, others do not. As the number of researchers starting to use microarrays and the number of cross-platform meta-analysis studies rapidly increases, appropriate platform assessments become more important. Here we present results from a comparison study that offers important improvements over those previously described in the literature. In particular, we noticed that none of the previously published papers consider differences between labs. For this study, a consortium of ten laboratories from the Washington, DC-Baltimore, USA, area was formed to compare data obtained from three widely used platforms using identical RNA samples. We used appropriate statistical analysis to demonstrate that there are relatively large differences in data obtained in labs using the same platform, but that the results from the best-performing labs agree rather well. Multiple-laboratory comparison of microarray platforms RA Irizarry D Warren F Spencer IF Kim S Biswal BC Frank E Gabrielson JG Garcia J Geoghegan G Germino C Griffin SC Hilmer E Hoffman AE Jedlicka E Kawasaki Martinez Murillo L Morsberger H Lee D Petersen J Quackenbush A Scott M Wilson Y Yang SQ Ye W Yu Nat Methods, Vol. 2, No. 5. (2005), pp. 345-50. 2006-02-23T18:37:28-00:00 2005 Nat Methods 2 5 345 50 all microarrays motivation http://www.citeulike.org/user/hpiwowar/article/518546 <i>Nat Genet, Vol. 29, No. 4. (2001), pp. 365-71.</i><br /><br />Microarray analysis has become a widely used tool for the generation of gene expression data on a genomic scale. Although many significant results have been derived from microarray studies, one limitation has been the lack of standards for presenting and exchanging such data. Here we present a proposal, the Minimum Information About a Microarray Experiment (MIAME), that describes the minimum information required to ensure that microarray data can be easily interpreted and that results derived from its analysis can be independently verified. The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools. With respect to MIAME, we concentrate on defining the content and structure of the necessary information rather than the technical format for capturing it. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data A Brazma P Hingamp J Quackenbush G Sherlock P Spellman C Stoeckert J Aach W Ansorge CA Ball HC Causton T Gaasterland P Glenisson FC Holstege IF Kim V Markowitz JC Matese H Parkinson A Robinson U Sarkans Schulze Kremer J Stewart R Taylor J Vilo M Vingron Nat Genet, Vol. 29, No. 4. (2001), pp. 365-71. 2006-02-23T18:37:24-00:00 2001 Nat Genet 29 4 365 71 all elpub miame microarrays standards