Multiple-laboratory comparison of microarray platforms

Rafael A. Irizarry, Daniel Warren, Forrest Spencer, Irene F. Kim, Shyam Biswal, Bryan C. Frank, Edward Gabrielson, Joe GN Garcia, Joel Geoghegan, Gregory Germino, Constance Griffin, Sara C. Hilmer, Eric Hoffman, Anne E. Jedlicka, Ernest Kawasaki, Francisco Martínez-Murillo, Laura Morsberger, Hannah Lee, David Petersen, John Quackenbush & 5 others Alan Scott, Michael Wilson, Yanqin Yang, Shui Qing Ye, Wayne Yu

Research output: Contribution to journalArticle

661 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)345-349
Number of pages5
JournalNature Methods
Volume2
Issue number5
DOIs
StatePublished - May 2005
Externally publishedYes

Fingerprint

Microarrays
RNA
Baltimore
Meta-Analysis
Statistical methods
Genes
Research Personnel
Technology
Gene Expression

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Cell Biology

Cite this

Irizarry, R. A., Warren, D., Spencer, F., Kim, I. F., Biswal, S., Frank, B. C., ... Yu, W. (2005). Multiple-laboratory comparison of microarray platforms. Nature Methods, 2(5), 345-349. https://doi.org/10.1038/nmeth756

Multiple-laboratory comparison of microarray platforms. / Irizarry, Rafael A.; Warren, Daniel; Spencer, Forrest; Kim, Irene F.; Biswal, Shyam; Frank, Bryan C.; Gabrielson, Edward; Garcia, Joe GN; Geoghegan, Joel; Germino, Gregory; Griffin, Constance; Hilmer, Sara C.; Hoffman, Eric; Jedlicka, Anne E.; Kawasaki, Ernest; Martínez-Murillo, Francisco; Morsberger, Laura; Lee, Hannah; Petersen, David; Quackenbush, John; Scott, Alan; Wilson, Michael; Yang, Yanqin; Ye, Shui Qing; Yu, Wayne.

In: Nature Methods, Vol. 2, No. 5, 05.2005, p. 345-349.

Research output: Contribution to journalArticle

Irizarry, RA, Warren, D, Spencer, F, Kim, IF, Biswal, S, Frank, BC, Gabrielson, E, Garcia, JGN, Geoghegan, J, Germino, G, Griffin, C, Hilmer, SC, Hoffman, E, Jedlicka, AE, Kawasaki, E, Martínez-Murillo, F, Morsberger, L, Lee, H, Petersen, D, Quackenbush, J, Scott, A, Wilson, M, Yang, Y, Ye, SQ & Yu, W 2005, 'Multiple-laboratory comparison of microarray platforms', Nature Methods, vol. 2, no. 5, pp. 345-349. https://doi.org/10.1038/nmeth756
Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC et al. Multiple-laboratory comparison of microarray platforms. Nature Methods. 2005 May;2(5):345-349. https://doi.org/10.1038/nmeth756
Irizarry, Rafael A. ; Warren, Daniel ; Spencer, Forrest ; Kim, Irene F. ; Biswal, Shyam ; Frank, Bryan C. ; Gabrielson, Edward ; Garcia, Joe GN ; Geoghegan, Joel ; Germino, Gregory ; Griffin, Constance ; Hilmer, Sara C. ; Hoffman, Eric ; Jedlicka, Anne E. ; Kawasaki, Ernest ; Martínez-Murillo, Francisco ; Morsberger, Laura ; Lee, Hannah ; Petersen, David ; Quackenbush, John ; Scott, Alan ; Wilson, Michael ; Yang, Yanqin ; Ye, Shui Qing ; Yu, Wayne. / Multiple-laboratory comparison of microarray platforms. In: Nature Methods. 2005 ; Vol. 2, No. 5. pp. 345-349.
@article{637897e2270c4d0b878aba05772a3d0c,
title = "Multiple-laboratory comparison of microarray platforms",
abstract = "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.",
author = "Irizarry, {Rafael A.} and Daniel Warren and Forrest Spencer and Kim, {Irene F.} and Shyam Biswal and Frank, {Bryan C.} and Edward Gabrielson and Garcia, {Joe GN} and Joel Geoghegan and Gregory Germino and Constance Griffin and Hilmer, {Sara C.} and Eric Hoffman and Jedlicka, {Anne E.} and Ernest Kawasaki and Francisco Mart{\'i}nez-Murillo and Laura Morsberger and Hannah Lee and David Petersen and John Quackenbush and Alan Scott and Michael Wilson and Yanqin Yang and Ye, {Shui Qing} and Wayne Yu",
year = "2005",
month = "5",
doi = "10.1038/nmeth756",
language = "English (US)",
volume = "2",
pages = "345--349",
journal = "Nature Methods",
issn = "1549-1277",
publisher = "Public Library of Science",
number = "5",

}

TY - JOUR

T1 - Multiple-laboratory comparison of microarray platforms

AU - Irizarry, Rafael A.

AU - Warren, Daniel

AU - Spencer, Forrest

AU - Kim, Irene F.

AU - Biswal, Shyam

AU - Frank, Bryan C.

AU - Gabrielson, Edward

AU - Garcia, Joe GN

AU - Geoghegan, Joel

AU - Germino, Gregory

AU - Griffin, Constance

AU - Hilmer, Sara C.

AU - Hoffman, Eric

AU - Jedlicka, Anne E.

AU - Kawasaki, Ernest

AU - Martínez-Murillo, Francisco

AU - Morsberger, Laura

AU - Lee, Hannah

AU - Petersen, David

AU - Quackenbush, John

AU - Scott, Alan

AU - Wilson, Michael

AU - Yang, Yanqin

AU - Ye, Shui Qing

AU - Yu, Wayne

PY - 2005/5

Y1 - 2005/5

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=18244384210&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=18244384210&partnerID=8YFLogxK

U2 - 10.1038/nmeth756

DO - 10.1038/nmeth756

M3 - Article

VL - 2

SP - 345

EP - 349

JO - Nature Methods

JF - Nature Methods

SN - 1549-1277

IS - 5

ER -