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1、TestingandevaluationofmicroarrayimageanalysissoftwareValutazionedisoftwaredianalisidimicroarraybasatosusimulazionidiimmaginidadatirealiIgnazioInfantinoTutorialsu“Metodiestrumentiperl’analisideidatidiespressionegenica”18Dicembre2007ICAR-CNRNapoliOverview
2、¢Introduction–AnalysisofMicroarrayimages•Addressingorgridding•Segmentation•Intensityextraction¢Microarrayresults:howaccuratearethey?¢Evaluationbysimulation–Statisticalanalysisofrealdata–SimulationModel–Testing–Anexampleofapplication¢Conclusions¢Referenc
3、esValutazionedisoftwaredianalisidimicroarray2Introduction¢cDNAmicroarraytechnologieshavelargediffusioninbiologicalresearchfield–Forstudyinggeneexpressioninmanydifferentorganism–Tolarge-scalegenediscovery–ForpolymorphismscreeningandmappingofgenomicDNAclo
4、nes¢Fullyautomatedandreliablesoftwareanalysissystemsarerequiredtoprocessthelargeamountofdataproduced¢EffectivetestingandevaluationofemployedcomputationalapproachesisstillanopenproblemC.C.Xiang,andY.Chen,“cDNAmicroarraytechnologyanditsapplications”,inBio
5、technologyAdvances,vol.18,2000,pp.35–46.Valutazionedisoftwaredianalisidimicroarray3MicroarraytechnologyValutazionedisoftwaredianalisidimicroarray4Analysisofmicroarrayimages¢Alaserscannerdetectssamplefluorescence–Cy3probeat532nm–Cy5probeat633nm¢CombinedR
6、GBcolorimagerepresentsdifferentiallyexpressedgenes–Thefluorescenceintensitiesarestoredas16-bitimageswhichweviewas“raw”data¢Imageprocessingsoftwareanalyzesredandgreenhybridizationintensitiesandred/greenratioforeverygeneonthearray,log(R/G)2Valutazionediso
7、ftwaredianalisidimicroarray5Analysisofmicroarrayimages(cntd)¢Thedigitalizationprocessproduces,foreachpixel,asignalthatrepresentsthetotalfluorescenceintheregioncorrespondingtothatpixel¢Whenproperlyprocessed,thissignalshouldcorrelatetotheareadensityofdyem
8、olecules¢Addressingorgridding¢Segmentation¢IntensityextractionY.H.Yang,M.J.BuckleyM,etal.,“ComparisonofmethodsforimageanalysisoncDNAmicroarraydata”,inJ.Comp.Graph.Stat.,11,2002,108-136Valutazionedisoftwaredianalisidimicroarray6Ad
