On the utility of pooling biological samples in microarray experiments

C. Kendziorski, R. A. Irizarry, K. S. Chen, J. D. Haag, M. N. Gould

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Pages (from-to)4252-4257
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume102
Issue number12
DOIs
StatePublished - Mar 22 2005

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Nucleic Acid Databases
Genes
Gene Expression
Data Accuracy
Datasets

ASJC Scopus subject areas

  • Genetics
  • General

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On the utility of pooling biological samples in microarray experiments. / Kendziorski, C.; Irizarry, R. A.; Chen, K. S.; Haag, J. D.; Gould, M. N.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 12, 22.03.2005, p. 4252-4257.

Research output: Contribution to journalArticle

Kendziorski, C. ; Irizarry, R. A. ; Chen, K. S. ; Haag, J. D. ; Gould, M. N. / On the utility of pooling biological samples in microarray experiments. In: Proceedings of the National Academy of Sciences of the United States of America. 2005 ; Vol. 102, No. 12. pp. 4252-4257.
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