On the utility of pooling biological samples in microarray experiments

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 micro...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS Vol. 102; no. 12; p. 4252
Main Authors: Kendziorski, C, Irizarry, R A, Chen, K-S, Haag, J D, Gould, M N
Format: Journal Article
Language:English
Published: United States 22.03.2005
Subjects:
Analysis of Variance
Animals
Female
Gene Expression Profiling - methods
Gene Expression Profiling - statistics & numerical data
Nicotinic Acids - pharmacology
Oligonucleotide Array Sequence Analysis - methods
Oligonucleotide Array Sequence Analysis - statistics & numerical data
Rats
Rats, Inbred WF
Retinoid X Receptors - agonists
RNA - genetics
Tetrahydronaphthalenes - pharmacology
ISSN:0027-8424
Online Access:Get more information
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Summary: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.
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ISSN:0027-8424
DOI:10.1073/pnas.0500607102