40 summarizeDetailsValueNumber of rows of object must match the length of probes.backgroundCorrectionMethods and normalizationMethods will return a character vector withthe methods implemented currently.backgroundCorrect, normalize and normalizeToTarget will return a matrix with same dimensionsas the input matrix. If they are applied to a FeatureSet object, the PM matrix will be used asinput.The summarize method will return a matrix with length(unique(probes)) rows and ncol(object)columns.Examplesns
Index∗Topic IOread.celfiles, 32read.xysfiles, 33∗Topic classesoligoPLM-class, 25∗Topic classifcrlmm, 8getNetAffx, 13runDate, 37∗Topic filelist.xysfiles, 19∗Topic hplotboxplot, 6darkColors, 9hist, 17image, 18MAplot, 20∗Topic loessMAplot, 20∗Topic manipbasecontent, 4basicPLM, 4basicRMA, 5chromosome, 7fitProbeLevelModel, 10getAffinitySplineCoefficients, 11getBaseProfile, 12getContainer, 12getCrlmmSummaries, 13getNgsColorsInfo, 14getPlatformDesign, 15getProbeInfo, 15getX, 16justSNPRMA, 19mm, 22mmindex, 23mmSequence, 24oligo-defunct, 24paCalls, 27pmAllele, 29pmFragmentLength, 30pmPosition, 30pmStrand, 31probeNames, 31readSummaries, 35sequenceDesignMatrix, 38snprma, 38summarize, 39∗Topic methodsboxplot, 6hist, 17MAplot, 20plotM-methods, 29rma-methods, 35∗Topic packageoligo-package, 3∗Topic smoothMAplot, 20annotation,oligoPLM-method(oligoPLM-class), 25availProbeInfo (getProbeInfo), 15backgroundCorrect (summarize), 39backgroundCorrect,FeatureSet-method(summarize), 39backgroundCorrect,ff_matrix-method(summarize), 39backgroundCorrect,matrix-method(summarize), 39backgroundCorrect-methods (summarize),39backgroundCorrectionMethods(summarize), 39basecontent, 4basicPLM, 4basicRMA, 5, 5bg (mm), 22bg,FeatureSet-method (mm), 2241