Assessing the reliability of amplified RNA used in microarrays: A DUMB table approach

Edward D. Bearden; Pippa M. Simpson; Charlotte A. Peterson; Marjorie L. Beggs

doi:10.2165/00822942-200605020-00001

Assessing the reliability of amplified RNA used in microarrays: A DUMB table approach

Edward D. Bearden
, Pippa M. Simpson
, Charlotte A. Peterson
, Marjorie L. Beggs

Physical Therapy

Producción científica: Article › revisión exhaustiva

2 Citas (Scopus)

Resumen

A certain minimal amount of RNA from biological samples is necessary to perform a microarray experiment with suitable replication. In some cases, the amount of RNA available is insufficient, necessitating RNA amplification prior to target synthesis. However, there is some uncertainty about the reliability of targets that have been generated from amplified RNA, because of nonlinearity and preferential amplification. This current work develops a straightforward strategy to assess the reliability of microarray data obtained from amplified RNA. The tabular method we developed, which utilises a Down-Up-Missing-Below (DUMB) classification scheme, shows that microarrays generated with amplified RNA targets are reliable within constraints. There was an increase in false negatives because of the need for increased filtering. Furthermore, this analysis method is generic and can be broadly applied to evaluate all microarray data. A copy of the Microsoft® Excel® spreadsheet is available upon request from Edward Bearden.

Idioma original	English
Páginas (desde-hasta)	67-76
Número de páginas	10
Publicación	Applied Bioinformatics
Volumen	5
N.º	2
DOI	https://doi.org/10.2165/00822942-200605020-00001
Estado	Published - 2006

Nota bibliográfica

Funding Information:
This research was supported in part by funds provided to the UAMS Microarray Facility through Act 1, The Arkansas Tobacco Settlement Proceeds Act of 2000, and by NIH grant no. P20 RR-16460 from the Biomedical Research Infrastructure Network (BRIN) Program of the National Center for Research Resources.

Financiación

This research was supported in part by funds provided to the UAMS Microarray Facility through Act 1, The Arkansas Tobacco Settlement Proceeds Act of 2000, and by NIH grant no. P20 RR-16460 from the Biomedical Research Infrastructure Network (BRIN) Program of the National Center for Research Resources.

Financiadores	Número del financiador
National Institutes of Health (NIH)
National Center for Research Resources	P20RR016460
University of Arkansas for Medical Sciences

ASJC Scopus subject areas

Information Systems
General Agricultural and Biological Sciences
Computer Science Applications

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10.2165/00822942-200605020-00001

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title = "Assessing the reliability of amplified RNA used in microarrays: A DUMB table approach",

abstract = "A certain minimal amount of RNA from biological samples is necessary to perform a microarray experiment with suitable replication. In some cases, the amount of RNA available is insufficient, necessitating RNA amplification prior to target synthesis. However, there is some uncertainty about the reliability of targets that have been generated from amplified RNA, because of nonlinearity and preferential amplification. This current work develops a straightforward strategy to assess the reliability of microarray data obtained from amplified RNA. The tabular method we developed, which utilises a Down-Up-Missing-Below (DUMB) classification scheme, shows that microarrays generated with amplified RNA targets are reliable within constraints. There was an increase in false negatives because of the need for increased filtering. Furthermore, this analysis method is generic and can be broadly applied to evaluate all microarray data. A copy of the Microsoft{\textregistered} Excel{\textregistered} spreadsheet is available upon request from Edward Bearden.",

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note = "Funding Information: This research was supported in part by funds provided to the UAMS Microarray Facility through Act 1, The Arkansas Tobacco Settlement Proceeds Act of 2000, and by NIH grant no. P20 RR-16460 from the Biomedical Research Infrastructure Network (BRIN) Program of the National Center for Research Resources.",

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AU - Bearden, Edward D.

AU - Simpson, Pippa M.

AU - Peterson, Charlotte A.

AU - Beggs, Marjorie L.

N1 - Funding Information: This research was supported in part by funds provided to the UAMS Microarray Facility through Act 1, The Arkansas Tobacco Settlement Proceeds Act of 2000, and by NIH grant no. P20 RR-16460 from the Biomedical Research Infrastructure Network (BRIN) Program of the National Center for Research Resources.

PY - 2006

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N2 - A certain minimal amount of RNA from biological samples is necessary to perform a microarray experiment with suitable replication. In some cases, the amount of RNA available is insufficient, necessitating RNA amplification prior to target synthesis. However, there is some uncertainty about the reliability of targets that have been generated from amplified RNA, because of nonlinearity and preferential amplification. This current work develops a straightforward strategy to assess the reliability of microarray data obtained from amplified RNA. The tabular method we developed, which utilises a Down-Up-Missing-Below (DUMB) classification scheme, shows that microarrays generated with amplified RNA targets are reliable within constraints. There was an increase in false negatives because of the need for increased filtering. Furthermore, this analysis method is generic and can be broadly applied to evaluate all microarray data. A copy of the Microsoft® Excel® spreadsheet is available upon request from Edward Bearden.

AB - A certain minimal amount of RNA from biological samples is necessary to perform a microarray experiment with suitable replication. In some cases, the amount of RNA available is insufficient, necessitating RNA amplification prior to target synthesis. However, there is some uncertainty about the reliability of targets that have been generated from amplified RNA, because of nonlinearity and preferential amplification. This current work develops a straightforward strategy to assess the reliability of microarray data obtained from amplified RNA. The tabular method we developed, which utilises a Down-Up-Missing-Below (DUMB) classification scheme, shows that microarrays generated with amplified RNA targets are reliable within constraints. There was an increase in false negatives because of the need for increased filtering. Furthermore, this analysis method is generic and can be broadly applied to evaluate all microarray data. A copy of the Microsoft® Excel® spreadsheet is available upon request from Edward Bearden.

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Assessing the reliability of amplified RNA used in microarrays: A DUMB table approach

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Financiación

ASJC Scopus subject areas

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