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Published online on March 8, 2005, 10.1073/pnas.0500607102
PNAS | March 22, 2005 | vol. 102 | no. 12 | 4252-4257
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STATISTICS / BIOCHEMISTRY
On the utility of pooling biological samples in microarray experiments

C. Kendziorski *, {dagger}, R. A. Irizarry {ddagger}, K.-S. Chen §, J. D. Haag §, and M. N. Gould §

*Department of Biostatistics and Medical Informatics and §McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI 53703; and {ddagger}Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205

Communicated by Grace Wahba, University of Wisconsin, Madison, WI, January 25, 2005 (received for review July 28, 2004)

Over 15% of the data sets catalogued in the Gene Expression Omnibus Database involve RNA samples that have been pooled before hybridization. Pooling affects data quality and inference, but the exact effects are not yet known because pooling has not been systematically studied in the context of microarray experiments. Here we report on the results of an experiment designed to evaluate the utility of pooling and the impact on identifying differentially expressed genes. We find that inference for most genes is not adversely affected by pooling, and we recommend that pooling be done when fewer than three arrays are used in each condition. For larger designs, pooling does not significantly improve inferences if few subjects are pooled. The realized benefits in this case do not outweigh the price paid for loss of individual specific information. Pooling is beneficial when many subjects are pooled, provided that independent samples contribute to multiple pools.

Author contributions: C.K. and R.A.I. designed research; J.D.H., K.S.C., and M.N.G. performed research; C.K. and R.A.I. analyzed data; C.K. obtained funds to conduct the experiments; and M.N.G. is head of the laboratory that ran this experiment.

Freely available online through the PNAS open access option.

Abbreviations: RMA, robust multiarray analysis; DE, differentially expressed; FDR, false discovery rate.

Data Deposition: The microarray data reported in this paper have been deposited in the Gene Expression Omnibus database (accession no. GSE2331).

{dagger} To whom correspondence should be addressed. E-mail: kendzior{at}biostat.wisc.edu.

© 2005 by The National Academy of Sciences of the USA


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