420 Title Convert Microarray Data Objects Author Gordon Smyth James Wettenhall Yee Hwa Jean Yang Martin Morgan Martin Morgan Maintainer Yee Hwa Jean Yang Depends R 260 Biobase 11533 limma 170 marray utils methods Description ID: 42326
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Package`convert'November14,2020Version1.66.0TitleConvertMicroarrayDataObjectsAuthorGordonSmyth&#xsmyt;&#xh@we;&#xhi.e; u.a;&#xu000;,JamesWettenhall&#xwett;nha;&#xll@w;hi.;íu.; u00;,YeeHwa(JeanYang)&#xjean;&#x@bio;&#xstat;&#x.ucs;.ed;&#xu000;,MartinMorgan&#xMart;&#xin.M;&#xorga;&#xn@Ro;&#xswel;&#xlPar;&#xk.or;&#xg000;MaintainerYeeHwa(Jean)Yang&#xjean;&#x@bio;&#xstat;&#x.ucs;.ed;&#xu000;DependsR&#xjean;&#x@bio;&#xstat;&#x.ucs;.ed;&#xu000;(=2.6.0),Biobase&#xjean;&#x@bio;&#xstat;&#x.ucs;.ed;&#xu000;(=1.15.33),limma&#xjean;&#x@bio;&#xstat;&#x.ucs;.ed;&#xu000;(=1.7.0),marray,utils,methodsDescriptionDenecoercemethodsformicroarraydataobjects.LicenseLGPLURLhttp://bioinf.wehi.edu.au/limma/convert.htmlbiocViewsInfrastructure,Microarray,TwoChannelgit_urlhttps://git.bioconductor.org/packages/convertgit_branchRELEASE_3_12git_last_commit73a5da9git_last_commit_date2020-10-27Date/Publication2020-11-13Rtopicsdocumented:coerce............................................1Index5 coerceConvertDataObjects DescriptionConvertbetweenlimma,marrayandBiobasedataobjects.1 2coerceDetailsObjectscanbeconverted(coerced)fromoneclasstoanotherusingas(object,Class)whereobjectisanobjecttoconvertandClassisthenameoftheclasstoconvertto.Thefollowingconversionsareprovided: coerce3From:To:RGListmarrayRawmarrayRawRGListMAListmarrayNormmarrayNormMAListRGListNChannelSetmarrayRawNChannelSetMAListExpressionSetmarrayNormExpressionSetRGListandmarrayRawarecoercedtoNChannelSet.Channelvaluesarenottransformed.MAListandmarrayNormarecoercedsothattheExpressionSetslotcontainslog-ratios(M-values)andtheExpressionSetobjecthasthesamenumberofcolumnsastheoriginalobject.Inthiscase,informationontheA-valuesislost.ThereisintentionallynoconversionfromRGListormarrayRawtoExpressionSet,asExpressionSetisintendedforexpressionvalues,notintensities.Author(s)GordonSmythandothersSeeAlsoasinthemethodspackage.Examples##firstsetupsomefakeintensitymatricestestRedmatrix(rnorm(5*2),5,2,dimnames=list(paste("gene",1:5,sep=""),c("S1","S2")))testGreenmatrix(rnorm(5*2),5,2,dimnames=list(paste("gene",1:5,sep=""),c("S1","S2")))##somesample/targetinfotestTargetdata.frame(slide=c("S1","S2"),Cy3=c("T","C"),Cy5=c("C","T"),row.names=c("S1","S2"))maTnew("marrayInfo",maLabels=c("S1","S2"),maInfo=testTarget)##nowcreateinstancesandconvertxnew("RGList")x$RtestRedx$GtestGreenyas(x,"marrayRaw")zas(x,"NChannelSet")xnew("marrayRaw")x@maGftestGreenx@maRftestRedx@maTargets=maTyas(x,"RGList")zas(x,"NChannelSet") 4coercexnew("MAList")yas(x,"marrayNorm")##weconstructareasonablycompletefake,small##instanceofthemarrayNormclassxnew("marrayNorm")x@maMtestRedx@maAtestGreenmaTargets(x)=maTyas(x,"MAList")yas(x,"ExpressionSet")xnew("MAList")x$MtestRedx$AtestGreenx$targetstestTargetyas(x,"ExpressionSet") Indexclassescoerce,1datacoerce,1as,3coerce,1coerce,MAList,ExpressionSet-method(coerce),1coerce,MAList,marrayNorm-method(coerce),1coerce,marrayNorm,ExpressionSet-method(coerce),1coerce,marrayNorm,MAList-method(coerce),1coerce,marrayRaw,NChannelSet-method(coerce),1coerce,marrayRaw,RGList-method(coerce),1coerce,RGList,marrayRaw-method(coerce),1coerce,RGList,NChannelSet-method(coerce),1convert(coerce),15