Standardizing global gene expression analysis between laboratories and across platforms. Export

@article{citeulike:238913, abstract = {To facilitate collaborative research efforts between multi-investigator teams using DNA microarrays, we identified sources of error and data variability between laboratories and across microarray platforms, and methods to accommodate this variability. RNA expression data were generated in seven laboratories, which compared two standard RNA samples using 12 microarray platforms. At least two standard microarray types (one spotted, one commercial) were used by all laboratories. Reproducibility for most platforms within any laboratory was typically good, but reproducibility between platforms and across laboratories was generally poor. Reproducibility between laboratories increased markedly when standardized protocols were implemented for RNA labeling, hybridization, microarray processing, data acquisition and data normalization. Reproducibility was highest when analysis was based on biological themes defined by enriched Gene Ontology (GO) categories. These findings indicate that microarray results can be comparable across multiple laboratories, especially when a common platform and set of procedures are used.}, author = {Bammler, T. and Beyer, R. P. and Bhattacharya, S. and Boorman, G. A. and Boyles, A. and Bradford, B. U. and Bumgarner, R. E. and Bushel, P. R. and Chaturvedi, K. and Choi, D. and Cunningham, M. L. and Deng, S. and Dressman, H. K. and Fannin, R. D. and Farin, F. M. and Freedman, J. H. and Fry, R. C. and Harper, A. and Humble, M. C. and Hurban, P. and Kavanagh, T. J. and Kaufmann, W. K. and Kerr, K. F. and Jing, L. and Lapidus, J. A. and Lasarev, M. R. and Li, J. and Li, Y. J. and Lobenhofer, E. K. and Lu, X. and Malek, R. L. and Milton, S. and Nagalla, S. R. and O'malley, J. P. and Palmer, V. S. and Pattee, P. and Paules, R. S. and Perou, C. M. and Phillips, K. and Qin, L. X. and Qiu, Y. and Quigley, S. D. and Rodland, M. and Rusyn, I. and Samson, L. D. and Schwartz, D. A. and Shi, Y. and Shin, J. L. and Sieber, S. O. and Slifer, S. and Speer, M. C. and Spencer, P. S. and Sproles, D. I. and Swenberg, J. A. and Suk, W. A. and Sullivan, R. C. and Tian, R. and Tennant, R. W. and Todd, S. A. and Tucker, C. J. and Van Houten, B. and Weis, B. K. and Xuan, S. and Zarbl, H. and {}}, citeulike-article-id = {238913}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nmeth754}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/15846362}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=15846362}, doi = {10.1038/nmeth754}, issn = {1548-7091}, journal = {Nat Methods}, keywords = {analyse, genomique, puces\_adn, stat, transcriptome}, month = {May}, number = {5}, pages = {351--356}, posted-at = {2005-06-27 19:57:35}, priority = {2}, title = {Standardizing global gene expression analysis between laboratories and across platforms.}, url = {http://dx.doi.org/10.1038/nmeth754}, volume = {2}, year = {2005} }

TY - JOUR ID - citeulike:238913 L3 - citeulike-article-id:238913 N2 - To facilitate collaborative research efforts between multi-investigator teams using DNA microarrays, we identified sources of error and data variability between laboratories and across microarray platforms, and methods to accommodate this variability. RNA expression data were generated in seven laboratories, which compared two standard RNA samples using 12 microarray platforms. At least two standard microarray types (one spotted, one commercial) were used by all laboratories. Reproducibility for most platforms within any laboratory was typically good, but reproducibility between platforms and across laboratories was generally poor. Reproducibility between laboratories increased markedly when standardized protocols were implemented for RNA labeling, hybridization, microarray processing, data acquisition and data normalization. Reproducibility was highest when analysis was based on biological themes defined by enriched Gene Ontology (GO) categories. These findings indicate that microarray results can be comparable across multiple laboratories, especially when a common platform and set of procedures are used. IS - 5 JF - Nat Methods SN - 1548-7091 EP - 356 TI - Standardizing global gene expression analysis between laboratories and across platforms. VL - 2 SP - 351 KW - analyse KW - genomique KW - puces_adn KW - stat KW - transcriptome AU - Bammler, T AU - Beyer, RP AU - Bhattacharya, S AU - Boorman, GA AU - Boyles, A AU - Bradford, BU AU - Bumgarner, RE AU - Bushel, PR AU - Chaturvedi, K AU - Choi, D AU - Cunningham, ML AU - Deng, S AU - Dressman, HK AU - Fannin, RD AU - Farin, FM AU - Freedman, JH AU - Fry, RC AU - Harper, A AU - Humble, MC AU - Hurban, P AU - Kavanagh, TJ AU - Kaufmann, WK AU - Kerr, KF AU - Jing, L AU - Lapidus, JA AU - Lasarev, MR AU - Li, J AU - Li, YJ AU - Lobenhofer, EK AU - Lu, X AU - Malek, RL AU - Milton, S AU - Nagalla, SR AU - O'malley, JP AU - Palmer, VS AU - Pattee, P AU - Paules, RS AU - Perou, CM AU - Phillips, K AU - Qin, LX AU - Qiu, Y AU - Quigley, SD AU - Rodland, M AU - Rusyn, I AU - Samson, LD AU - Schwartz, DA AU - Shi, Y AU - Shin, JL AU - Sieber, SO AU - Slifer, S AU - Speer, MC AU - Spencer, PS AU - Sproles, DI AU - Swenberg, JA AU - Suk, WA AU - Sullivan, RC AU - Tian, R AU - Tennant, RW AU - Todd, SA AU - Tucker, CJ AU - Van Houten, B AU - Weis, BK AU - Xuan, S AU - Zarbl, H PY - 2005/05// UR - http://dx.doi.org/10.1038/nmeth754 ER -