Display options
Cite
Bammler T, Beyer RP, Bhattacharya S, et al. Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods. 2005;2(5):351-6doi: 10.1038/nmeth754.
Bammler, T., Beyer, R. P., Bhattacharya, S., Boorman, G. A., Boyles, A., Bradford, B. U., Bumgarner, R. E., Bushel, P. R., Chaturvedi, K., Choi, D., Cunningham, M. L., Deng, S., Dressman, H. K., Fannin, R. D., Farin, F. M., Freedman, J. H., Fry, R. C., Harper, A., Humble, M. C., Hurban, P., Kavanagh, T. J., Kaufmann, W. K., Kerr, K. F., Jing, L., Lapidus, J. A., Lasarev, M. R., Li, J., Li, Y. J., Lobenhofer, E. K., Lu, X., Malek, R. L., Milton, S., Nagalla, S. R., O'malley, J. P., Palmer, V. S., Pattee, P., Paules, R. S., Perou, C. M., Phillips, K., Qin, L. X., Qiu, Y., Quigley, S. D., Rodland, M., Rusyn, I., Samson, L. D., Schwartz, D. A., Shi, Y., Shin, J. L., Sieber, S. O., Slifer, S., Speer, M. C., Spencer, P. S., Sproles, D. I., Swenberg, J. A., Suk, W. A., Sullivan, R. C., Tian, R., Tennant, R. W., Todd, S. A., Tucker, C. J., Van Houten, B., Weis, B. K., Xuan, S., Zarbl, H. (2005). Standardizing global gene expression analysis between laboratories and across platforms. Nature methods, 2(5), 351-6. https://doi.org/10.1038/nmeth754
Bammler, Theodore, et al. "Standardizing global gene expression analysis between laboratories and across platforms." Nature methods vol. 2,5 (2005): 351-6. doi: https://doi.org/10.1038/nmeth754
Bammler T, Beyer RP, Bhattacharya S, Boorman GA, Boyles A, Bradford BU, Bumgarner RE, Bushel PR, Chaturvedi K, Choi D, Cunningham ML, Deng S, Dressman HK, Fannin RD, Farin FM, Freedman JH, Fry RC, Harper A, Humble MC, Hurban P, Kavanagh TJ, Kaufmann WK, Kerr KF, Jing L, Lapidus JA, Lasarev MR, Li J, Li YJ, Lobenhofer EK, Lu X, Malek RL, Milton S, Nagalla SR, O'malley JP, Palmer VS, Pattee P, Paules RS, Perou CM, Phillips K, Qin LX, Qiu Y, Quigley SD, Rodland M, Rusyn I, Samson LD, Schwartz DA, Shi Y, Shin JL, Sieber SO, Slifer S, Speer MC, Spencer PS, Sproles DI, Swenberg JA, Suk WA, Sullivan RC, Tian R, Tennant RW, Todd SA, Tucker CJ, Van Houten B, Weis BK, Xuan S, Zarbl H. Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods. 2005 May;2(5):351-6. doi: 10.1038/nmeth754. Epub 2005 Apr 21. PMID: 15846362.
Copy Download .nbib Format: NLM
Share it on

Nat Methods. 2005 May;2(5):351-6. doi: 10.1038/nmeth754. Epub 2005 Apr 21.

Standardizing global gene expression analysis between laboratories and across platforms.

Nature methods

Theodore Bammler, Richard P Beyer, Sanchita Bhattacharya, Gary A Boorman, Abee Boyles, Blair U Bradford, Roger E Bumgarner, Pierre R Bushel, Kabir Chaturvedi, Dongseok Choi, Michael L Cunningham, Shibing Deng, Holly K Dressman, Rickie D Fannin, Fredrico M Farin, Jonathan H Freedman, Rebecca C Fry, Angel Harper, Michael C Humble, Patrick Hurban, Terrance J Kavanagh, William K Kaufmann, Kathleen F Kerr, Li Jing, Jodi A Lapidus, Michael R Lasarev, Jianying Li, Yi-Ju Li, Edward K Lobenhofer, Xinfang Lu, Renae L Malek, Sean Milton, Srinivasa R Nagalla, Jean P O'malley, Valerie S Palmer, Patrick Pattee, Richard S Paules, Charles M Perou, Ken Phillips, Li-Xuan Qin, Yang Qiu, Sean D Quigley, Matthew Rodland, Ivan Rusyn, Leona D Samson, David A Schwartz, Yan Shi, Jung-Lim Shin, Stella O Sieber, Susan Slifer, Marcy C Speer, Peter S Spencer, Dean I Sproles, James A Swenberg, William A Suk, Robert C Sullivan, Ru Tian, Raymond W Tennant, Signe A Todd, Charles J Tucker, Bennett Van Houten, Brenda K Weis, Shirley Xuan, Helmut Zarbl,

PMID: 15846362 DOI: 10.1038/nmeth754

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.

MeSH terms

Publication Types

Grant support