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    The utility of MAS5 expression summary and detection call algorithms.

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    Authors
    Pepper, Stuart D
    Saunders, Emma K
    Edwards, Laura E
    Wilson, Claire L
    Miller, Crispin J
    Affiliation
    Cancer Research UK, Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital Site, Withington, Manchester, UK. spepper@picr.man.ac.uk <spepper@picr.man.ac.uk>
    Issue Date
    2007-07-30
    
    Metadata
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    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.
    Citation
    The utility of MAS5 expression summary and detection call algorithms. 2007, 8:273 BMC Bioinformatics
    Journal
    BMC Bioinformatics
    URI
    http://hdl.handle.net/10541/70374
    DOI
    10.1186/1471-2105-8-273
    PubMed ID
    17663764
    Type
    Article
    Language
    en
    ISSN
    1471-2105
    ae974a485f413a2113503eed53cd6c53
    10.1186/1471-2105-8-273
    Scopus Count
    Collections
    All Paterson Institute for Cancer Research

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