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

Research output: Contribution to journalArticlepeer-review

2 Scopus citations


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.

Original languageEnglish
Pages (from-to)67-76
Number of pages10
JournalApplied Bioinformatics
Issue number2
StatePublished - 2006

Bibliographical 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.

ASJC Scopus subject areas

  • Information Systems
  • General Agricultural and Biological Sciences
  • Computer Science Applications


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