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dc.contributor.authorPepper, Stuart D
dc.contributor.authorSaunders, Emma K
dc.contributor.authorEdwards, Laura E
dc.contributor.authorWilson, Claire L
dc.contributor.authorMiller, Crispin J
dc.date.accessioned2009-06-12T14:10:25Z
dc.date.available2009-06-12T14:10:25Z
dc.date.issued2007-07-30
dc.identifier.citationThe utility of MAS5 expression summary and detection call algorithms. 2007, 8:273 BMC Bioinformaticsen
dc.identifier.issn1471-2105
dc.identifier.pmid17663764
dc.identifier.doi10.1186/1471-2105-8-273
dc.identifier.urihttp://hdl.handle.net/10541/70374
dc.description.abstractBACKGROUND: 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.
dc.language.isoenen
dc.subject.meshAlgorithms
dc.subject.meshGene Expression Profiling
dc.subject.meshOligonucleotide Array Sequence Analysis
dc.subject.meshReproducibility of Results
dc.subject.meshSensitivity and Specificity
dc.subject.meshSoftware
dc.subject.meshSoftware Validation
dc.titleThe utility of MAS5 expression summary and detection call algorithms.en
dc.typeArticleen
dc.contributor.departmentCancer 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>en
dc.identifier.journalBMC Bioinformaticsen
html.description.abstractBACKGROUND: 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.


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