SupplementaryMaterialCurrentMetabolomics,2013,Vol.1,No.2iSupplementaryMaterialMetabolomicUnivariate&MultivariateAnalysis(muma)TUTORIALiiCurrentMetabolomics,2013,Vol.1,No.2SupplementaryMaterialTABLEOFCONTENTSmumaoverview..............................................................................3Functionslist..................................................................................3DownloadandInstallation...............................................................4Datasetformat...............................................................................5Analysisprocedure.........................................................................51|Createtheworkingdirectory.....................................................................62|Starttheanalysis.......................................................................................63|PrincipalComponentAnalysis–ScoreandLoadingplots.......................114|UnivariateAnalysis..................................................................................135|Mergeunivariateandmultivariateinformation.......................................176|PartialLeastSquareDiscriminantAnalysis(PLS-DA)..............................197|OrthogonalProjectiontoLatentStructures-DiscriminantAnalysis(OPLS-DA)..............................................................................................................208|ToolsforNMRmolecularassignmentanddatainterpretation..............21A|StatisticalTOtalCorrelationSpectroscopY(STOCSY).......................21B|STOCSY1D.........................................................................................23C|OrthogonalSignalCorrection(OSC)–STOCSY...................................24D|RatioAnalysisNMRSpectroscopY(RANSY)........................................26References...................................................................................27SupplementaryMaterialCurrentMetabolomics,2013,Vol.1,No.2iiimumaoverviewmumaisatoolforthemultivariateandunivariatestatisticalanalysisofmetabolomicdata,writtenintheformofadd-onpackagefortheopensourcesoftwareR.Bycreatingthisstatisticalprotocolwewantedtoprovideguidelinesforthewholeprocessofmetabolomicdatainterpretation,fromdatapre-processing,todatasetexplorationandvisualization,toidentificationofpotentiallyinterestingvariables(ormetabolites).Fordoingso,weimplementedthestepsthataretypicallyusedinmetabolomicanalysesandcreatedsomenewtipsthatcanfacilitateuser’swork.Infact,mumaisdesignedforthosepeoplewhoarenotRexperts,butwanttoperformstatisticalanalysisinaveryshorttimeandwithreliableresults.Eventhoughmumahasbeendesignedfortheanalysisofmetabolomicdatageneratedwithdifferentanalyticalplatforms(NMR,MS,NIR..),itprovidesspecificmethodsforhelpingtheNMR-basedmetabolomics.Inparticular,mumaisequippedwithtwotools(STOCSYandRANSY)aidingtheidentificationandassignmentofmoleculespresentinNMRspectra,orsuggestingpossiblebiochemicalinteractionbetweendifferentmolecules.Inthistutorialweprovideaworkflowformetabolomicsdatainterpretationusingmuma,describingfromtheinstallationtothespecificusageofallmuma’sfunctions,totherecoveryofallresultsgenerated.Enjoy.Functionslistwork.dir()Generateaworkingdirectorywithinwhichallthefilesgeneratedarestored.explore.data()Performdatapre-processing(normalization,scaling)anddataexploration,throughPCA.Plot.pca()Plotthe...
