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Open Access Highly Accessed Research article

The utility of MAS5 expression summary and detection call algorithms

Stuart D Pepper1, Emma K Saunders1, Laura E Edwards1, Claire L Wilson12 and Crispin J Miller1*

Author Affiliations

1 Cancer Research UK, Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital Site, Wilmslow Road, Withington, Manchester, M20 4BX, UK

2 Epistem Ltd, 48 Grafton Street, Manchester, M13 9XX, UK

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BMC Bioinformatics 2007, 8:273  doi:10.1186/1471-2105-8-273

Published: 30 July 2007

Abstract

Background

Used alone, the MAS5.0 algorithm for generating expression summaries has been criticized for high False Positive rates resulting from exaggerated variance at low intensities.

Results

Here we show, with replicated cell line data, that, when used alongside detection calls, MAS5 can be both selective and sensitive. A set of differentially expressed transcripts were identified that were found to be changing by MAS5, but unchanging by RMA and GCRMA. Subsequent analysis by real time PCR confirmed these changes. In addition, with the Latin square datasets often used to assess expression summary algorithms, filtered MAS5.0 was found to have performance approaching that of its peers.

Conclusion

When used alongside detection calls, MAS5 is a sensitive and selective algorithm for identifying differentially expressed genes.