2.50
Hdl Handle:
http://hdl.handle.net/10541/70374
Title:
The utility of MAS5 expression summary and detection call algorithms.
Authors:
Pepper, Stuart D; Saunders, Emma K; Edwards, Laura E; Wilson, Claire L; Miller, Crispin J
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.
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>
Citation:
The utility of MAS5 expression summary and detection call algorithms. 2007, 8:273 BMC Bioinformatics
Journal:
BMC Bioinformatics
Issue Date:
30-Jul-2007
URI:
http://hdl.handle.net/10541/70374
DOI:
10.1186/1471-2105-8-273
PubMed ID:
17663764
Type:
Article
Language:
en
ISSN:
1471-2105
Appears in Collections:
All Paterson Institute for Cancer Research

Full metadata record

DC FieldValue Language
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.en
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

Related articles on PubMed

All Items in Christie are protected by copyright, with all rights reserved, unless otherwise indicated.