Standardizing global gene expression analysis between laboratories and across platforms.
Journal Article (Journal Article)
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.
Full Text
Duke Authors
Cited Authors
- 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, Y-J; Lobenhofer, EK; Lu, X; Malek, RL; Milton, S; Nagalla, SR; O'malley, JP; Palmer, VS; Pattee, P; Paules, RS; Perou, CM; Phillips, K; Qin, L-X; Qiu, Y; Quigley, SD; Rodland, M; Rusyn, I; Samson, LD; Schwartz, DA; Shi, Y; Shin, J-L; 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; Members of the Toxicogenomics Research Consortium,
Published Date
- May 2005
Published In
Volume / Issue
- 2 / 5
Start / End Page
- 351 - 356
PubMed ID
- 15846362
International Standard Serial Number (ISSN)
- 1548-7091
Digital Object Identifier (DOI)
- 10.1038/nmeth754
Language
- eng
Conference Location
- United States