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Analysis of High-Throughput Flow Cytometry Data Using plateCore英文文献资料.doc

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Analysis of High-Throughput Flow Cytometry Data Using plateCore英文文献资料

HindawiPublishingCorporation AdvancesinBioinformatics Volume2009,ArticleID356141,10pages doi:10.1155/2009/356141 ResearchArticle AnalysisofHigh-ThroughputFlowCytometryData UsingplateCore ErrolStrain, FlorianHahne, RyanR.Brinkman, andPerryHaaland 1 2 3 4 1 2 3 4 FDA-CenterforFoodSafetyandNutrition,HFS-0135100PaintBranchParkway,CollegePark,MD20740,USA FredHutchisonCancerResearchCenter,M2-B514P.O.Box19024Seattle,WA98109,USA TerryFoxLaboratory,BritishColumbiaCancerAgency,675West10thAvenue,Vancouver,BC,CanadaV5Z1L3 BDTechnologies,21DavisDr,ResearchTrianglePark,NC27709,USA CorrespondenceshouldbeaddressedtoErrolStrain,estrain@ Received2April2009;Accepted21July2009 RecommendedbyMattWand Flowcytometry(FCM)softwarepackagesfromR/Bioconductor,suchas?owCoreand?owViz,serveasanopenplatformfor developmentofnewanalysistoolsandmethods.WecreatedplateCore,anewpackagethatextendsthefunctionalityinthese corepackagestoenableautomatednegativecontrol-basedgatingandmaketheprocessingandanalysisofplate-baseddatasets fromhigh-throughputFCMscreeningexperimentseasier.plateCorewasusedtoanalyzedatafromaBDFACSCAPscreening experimentwhere?vePeripheralBloodMononucleocyteCell(PBMC)sampleswereassayedfor189di?erenthumancellsurface markers.ThissamedatasetwasalsomanuallyanalyzedbyacytometryexpertusingtheFlowJodataanalysissoftwarepackage (TreeStar,USA).WeshowthattheexpressionvaluesformarkerscharacterizedusingtheautomatedapproachinplateCorearein goodagreementwiththosefromFlowJo,andthatusingplateCoreallowsformorereproducibleanalysesofFCMscreeningdata. Copyright?2009ErrolStrainetal.ThisisanopenaccessarticledistributedundertheCreativeCommonsAttributionLicense, whichpermitsunrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalworkisproperlycited. 1.Introduction FCM data so that FC-HCS analysis pipelines are robust, objective, and ableto match thehigh-throughput capacity ofmoderncytometers. While there are a number of di?erent software