Assessing the reliability of amplified RNA used in microarrays: a DUMB table approach. Appl Bioinformatics 2006;5(2):67-76
Date
05/26/2006Pubmed ID
16722771DOI
10.2165/00822942-200605020-00001Scopus ID
2-s2.0-33744935243 (requires institutional sign-in at Scopus site) 2 CitationsAbstract
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.
Author List
Bearden ED, Simpson PM, Peterson CA, Beggs MLAuthor
Pippa M. Simpson PhD Adjunct Professor in the Pediatrics department at Medical College of WisconsinMESH terms used to index this publication - Major topics in bold
BenzothiazolesCell Line, Tumor
Computational Biology
Diamines
False Negative Reactions
Humans
Models, Statistical
Oligonucleotide Array Sequence Analysis
Oligonucleotides
Organic Chemicals
Quinolines
RNA
Reproducibility of Results
Reverse Transcriptase Polymerase Chain Reaction
