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Arrow plot and correspondence analysis maps for visualizing the effects of background correction and normalization methods on microarray data

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dc.contributor.authorSilva, Carina
dc.contributor.authorFreitas, Adelaide
dc.contributor.authorRoque, Sara
dc.contributor.authorSousa, Lisete
dc.date.accessioned2016-12-22T18:49:05Z
dc.date.available2016-12-22T18:49:05Z
dc.date.issued2016
dc.description.abstractAmong various available array technologies, double-channel cDNA microarray experiments provide numerous technical protocols associated with functional genomic studies. The chapter begins by detailing the arrow plot, which is a recent graphical-based methodology to detect differentially expressed (DE) genes, and briefly mentions the significance analysis of microarrays (SAM) procedure, which is, in contrast, quite well known. Next, it introduces the correspondence analysis (CA) and explains how the resultant graphic can be interpreted. Then, CA in both class comparison and class prediction applications and over the data sets lymphoma (lym), lung (lun), and liver (liv) is executed. The CA is applied to all three databases in order to obtain graphical representations of background correction (BC) and normalization (NM) profiles in a two-dimensional reduced space. Whenever possible, more than one preprocessing strategy on microarray data could be applied and results from preprocessed data should be compared before any conclusion and subsequent analysis.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationSilva C, Freitas A, Roque S, Sousa L. Arrow plot and correspondence analysis maps for visualizing the effects of background correction and normalization methods on microarray data. In: Elloumi M, Iliopoulos C, Wang JT, Zomaya AY, editors. Pattern recognition in computational molecular biology: techniques and approaches. Wiley; 2016. p. 394-416.pt_PT
dc.identifier.doi10.1002/9781119078845.ch21pt_PT
dc.identifier.isbn9781118893685
dc.identifier.urihttp://hdl.handle.net/10400.21/6670
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherWileypt_PT
dc.relation.publisherversionhttp://onlinelibrary.wiley.com/doi/10.1002/9781119078845.ch21/summarypt_PT
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/pt_PT
dc.subjectArrow plotpt_PT
dc.subjectBackground correction methodspt_PT
dc.subjectCorrespondence analysispt_PT
dc.subjectDifferentially expressed genespt_PT
dc.subjectMicroarray datapt_PT
dc.subjectNormalization methodspt_PT
dc.subjectSignificance analysis of microarrayspt_PT
dc.titleArrow plot and correspondence analysis maps for visualizing the effects of background correction and normalization methods on microarray datapt_PT
dc.typebook part
dspace.entity.typePublication
oaire.citation.endPage416pt_PT
oaire.citation.startPage394pt_PT
rcaap.rightsrestrictedAccesspt_PT
rcaap.typebookPartpt_PT

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