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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| Published in | Proceedings of the National Academy of Sciences - PNAS Vol. 102; no. 12; pp. 4252 - 4257 |
|---|---|
| Main Authors | , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
National Academy of Sciences
22.03.2005
National Acad Sciences |
| Subjects | |
| Online Access | Get full text |
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| 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. |
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| AbstractList | 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. 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.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 | Haag, J. D. Wahba, Grace K.-S. Chen Gould, M. N. Kendziorski, C. Irizarry, R. A. |
| AuthorAffiliation | Department of Biostatistics and Medical Informatics and § McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI 53703; and ‡ Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205 |
| AuthorAffiliation_xml | – name: Department of Biostatistics and Medical Informatics and § McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI 53703; and ‡ Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205 |
| Author_xml | – sequence: 1 givenname: C. surname: Kendziorski fullname: Kendziorski, C. – sequence: 2 givenname: R. A. surname: Irizarry fullname: Irizarry, R. A. – sequence: 3 fullname: K.-S. Chen – sequence: 4 givenname: J. D. surname: Haag fullname: Haag, J. D. – sequence: 5 givenname: M. N. surname: Gould fullname: Gould, M. N. – sequence: 6 givenname: Grace surname: Wahba fullname: Wahba, Grace |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/15755808$$D View this record in MEDLINE/PubMed |
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| Copyright | Copyright 1993/2005 The National Academy of Sciences of the United States of America Copyright © 2005, The National Academy of Sciences 2005 |
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| Notes | ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 23 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). 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. To whom correspondence should be addressed. E-mail: kendzior@biostat.wisc.edu. Communicated by Grace Wahba, University of Wisconsin, Madison, WI, January 25, 2005 |
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| Snippet | Over 15% of the data sets catalogued in the Gene Expression Omnibus Database involve RNA samples that have been pooled before hybridization. Pooling affects... |
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| SubjectTerms | Analysis of Variance Animals Arithmetic mean Biological Sciences Biostatistics Datasets Diet Experiment design Female Gene expression Gene Expression Profiling - methods Gene Expression Profiling - statistics & numerical data Genes Nicotinic Acids - pharmacology Oligonucleotide Array Sequence Analysis - methods Oligonucleotide Array Sequence Analysis - statistics & numerical data Physical Sciences Rats Rats, Inbred WF Retinoid X Receptors - agonists RNA RNA - genetics Statistical variance Statistics Tetrahydronaphthalenes - pharmacology |
| Title | On the Utility of Pooling Biological Samples in Microarray Experiments |
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