Bridging the Divide between Manual Gating and Bioinformatics with the Bioconductor Package flowFlowJo英文文献资料.docVIP

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Bridging the Divide between Manual Gating and Bioinformatics with the Bioconductor Package flowFlowJo英文文献资料.doc

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Bridging the Divide between Manual Gating and Bioinformatics with the Bioconductor Package flowFlowJo英文文献资料

HindawiPublishingCorporation AdvancesinBioinformatics Volume2009,ArticleID809469,8pages doi:10.1155/2009/809469 ResearchArticle BridgingtheDividebetweenManualGatingand BioinformaticswiththeBioconductorPackage?owFlowJo JohnJ.Gosink, GaryD.Means, WilliamA.Rees, ChengSu, andHughA.Rand 1 2 2 3 1 1 2 3 DepartmentofComputationalBiology,Amgen,1201AmgenCourtWest,Seattle,WA98119,USA DepartmentofMolecularSciences,Amgen,1201AmgenCourtWest,Seattle,WA98119,USA DepartmentofBiostatistics—MedicalSciences,Amgen,1201AmgenCourtWest,Seattle,WA98119,USA CorrespondenceshouldbeaddressedtoHughA.Rand,rand@ Received31March2009;Revised19June2009;Accepted19July2009 RecommendedbyRaphaelGottardo In ?ow cytometry, di?erent cell types are usually selected or “gated” by a series of 1- or 2-dimensional geometric subsets of themeasurementsmadeoneachcell.Thisiseasilyaccomplishedincommercial?owcytometry packagesbutitisdi?cultto workcomputationallywiththeresultsofthisprocess.Theabilitytoretrievetheresultsandworkwithboththemandtheraw dataiscritical;ourexperiencepointstotheimportanceofbioinformaticstoolsthatwillallowustoexaminegatingrobustness, combinemanualandautomatedgating,andperformexploratorydataanalysis.Toprovidethiscapability,wehavedevelopeda Bioconductorpackagecalled?owFlowJothatcanimportgatesde?nedbythecommercialpackageFlowJoandworkwiththem inamannerconsistentwiththeother?owpackagesinBioconductor.Wepresentthispackageandillustratesomeofthewaysin whichitcanbeused. Copyright?2009JohnJ.Gosinketal.ThisisanopenaccessarticledistributedundertheCreativeCommonsAttributionLicense, whichpermitsunrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalworkisproperlycited. 1.Introduction data,(2)toolsfordataorganization,annotation,andquery, (3) tools for data manipulation, and (4) techniques and statisticalmethodsfordataanalysis.Allofthesecomponents are related and, done well, serve to reinforce each other. The?rsttwoofthe