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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| Vydané v: | Proceedings of the National Academy of Sciences - PNAS Ročník 102; číslo 12; s. 4252 |
|---|---|
| Hlavní autori: | , , , , |
| Médium: | Journal Article |
| Jazyk: | English |
| Vydavateľské údaje: |
United States
22.03.2005
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| Predmet: | |
| ISSN: | 0027-8424 |
| On-line prístup: | Zistit podrobnosti o prístupe |
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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 | Kendziorski, C Irizarry, R A Chen, K-S Haag, J D Gould, M N |
| Author_xml | – sequence: 1 givenname: C surname: Kendziorski fullname: Kendziorski, C email: kendzior@biostat.wisc.edu organization: Department of Biostatistics and Medical Informatics and McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI 53703, USA. kendzior@biostat.wisc.edu – sequence: 2 givenname: R A surname: Irizarry fullname: Irizarry, R A – sequence: 3 givenname: K-S surname: Chen fullname: Chen, K-S – sequence: 4 givenname: J D surname: Haag fullname: Haag, J D – sequence: 5 givenname: M N surname: Gould fullname: Gould, M N |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/15755808$$D View this record in MEDLINE/PubMed |
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| References | 12883005 - Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9440-5 11929952 - J Natl Cancer Inst. 2002 Apr 3;94(7):513-21 12823867 - BMC Bioinformatics. 2003 Jun 24;4:26 16646809 - Stat Appl Genet Mol Biol. 2004;3:Article3 12925512 - Biostatistics. 2003 Jul;4(3):465-77 11509024 - Toxicol Appl Pharmacol. 2001 Aug 15;175(1):28-42 11389458 - Nat Rev Genet. 2001 Jun;2(6):418-27 12567189 - Nat Genet. 2003 Mar;33(3):422-5 11382364 - J Comput Biol. 2000;7(6):819-37 15071073 - J Gerontol A Biol Sci Med Sci. 2004 Apr;59(4):306-15 11747616 - J Comput Biol. 2001;8(6):625-37 14673946 - Stat Med. 2003 Dec 30;22(24):3899-914 11721059 - Science. 2001 Nov 23;294(5547):1731-5 12582260 - Nucleic Acids Res. 2003 Feb 15;31(4):e15 12925520 - Biostatistics. 2003 Apr;4(2):249-64 11951044 - Science. 2002 Apr 12;296(5566):340-3 12454643 - Nat Genet. 2002 Dec;32 Suppl:490-5 11842121 - Nucleic Acids Res. 2002 Feb 15;30(4):e15 11726925 - Nat Genet. 2001 Dec;29(4):389-95 11726914 - Nat Genet. 2001 Dec;29(4):355-6 11285368 - Physiol Genomics. 2001 Apr 2;5(3):147-60 |
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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 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 |
| Title | On the utility of pooling biological samples in microarray experiments |
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