Entry: [-methods
Aliases: [-methods [
Keywords: methods
Description: Subsetting methods for microarray objects
URL: ../../../library/marrayClasses/html/[-methods.html

Entry: coerce-methods
Aliases: coerce-methods coerce as
Keywords: methods
Description: Coerce an object to belong to a given microarray class
URL: ../../../library/marrayClasses/html/coerce-methods.html

Entry: maCompCoord
Aliases: maCompCoord
Keywords: manip methods
Description: Generate grid and spot matrix coordinates
URL: ../../../library/marrayClasses/html/maCompCoord.html

Entry: maCompInd
Aliases: maCompInd
Keywords: manip methods
Description: Generate spot indices
URL: ../../../library/marrayClasses/html/maCompInd.html

Entry: maCompPlate
Aliases: maCompPlate
Keywords: methods
Description: Generate plate IDs
URL: ../../../library/marrayClasses/html/maCompPlate.html

Entry: maCoord2Ind
Aliases: maCoord2Ind
Keywords: manip methods
Description: Convert grid and spot matrix coordinates to spot indices
URL: ../../../library/marrayClasses/html/maCoord2Ind.html

Entry: maDotsMatch
Aliases: maDotsMatch
Keywords: misc
Description: Replace default arguments of a function by user supplied values
URL: ../../../library/marrayClasses/html/maDotsMatch.html

Entry: maGenControls
Aliases: maGenControls controlCode
Keywords: manip
Description: Generating a vector recording the control status of the spotted probe sequences.
URL: ../../../library/marrayClasses/html/maGenControls.html

Entry: maGeneTable
Aliases: maGeneTable
Keywords: methods
Description: Table of spot coordinates and gene names
URL: ../../../library/marrayClasses/html/maGeneTable.html

Entry: maInd2Coord
Aliases: maInd2Coord
Keywords: manip methods
Description: Convert spot indices to grid and spot matrix coordinates
URL: ../../../library/marrayClasses/html/maInd2Coord.html

Entry: maNum2Logic
Aliases: maNum2Logic
Keywords: manip
Description: Convert a numeric vector of indices to a logical vector
URL: ../../../library/marrayClasses/html/maNum2Logic.html

Entry: marrayInfo-class
Aliases: marrayInfo-class marrayInfo maLabels maLabels<- maInfo maInfo<- maNotes maNotes<- [,marrayInfo-method maGnames<-,marrayRaw,marrayInfo-method maGnames<-,marrayNorm,marrayInfo-method maGnames<-,marraySpots,marrayInfo-method maInfo<-,marrayInfo,data.frame-method maInfo,marrayInfo-method maLabels<-,marrayInfo,character-method maLabels<-,marrayInfo,numeric-method maLabels,marrayInfo-method maNotes<-,marrayInfo,character-method maNotes,marrayInfo-method maTargets<-,marrayRaw,marrayInfo-method maTargets<-,marrayNorm,marrayInfo-method maTargets<-,marrayTwo,marrayInfo-method print,marrayInfo-method rbind,marrayInfo-method show,marrayInfo-method
Keywords: classes
Description: Class "marrayInfo", description of target samples or spotted probe sequences
URL: ../../../library/marrayClasses/html/marrayInfo-class.html

Entry: marrayLayout-class
Aliases: marrayLayout-class marrayLayout maNgr maNgr<- maNgc maNgc<- maNsr maNsr<- maNsc maNsc<- maNspots maNspots<- maSub maSub<- maPlate maPlate<- maControls maControls<- [,marrayLayout-method maControls<-,marrayLayout-method maControls,marrayLayout-method maGridCol,marrayLayout-method maGridRow,marrayLayout-method maLayout<-,marrayRaw,marrayLayout-method maLayout<-,marrayNorm,marrayLayout-method maLayout<-,marraySpots,marrayLayout-method maLayout<-,marrayTwo,marrayLayout-method maNgc<-,marrayLayout,numeric-method maNgc,marrayLayout-method maNgr<-,marrayLayout,numeric-method maNgr,marrayLayout-method maNotes<-,marrayLayout,character-method maNotes,marrayLayout-method maNsc<-,marrayLayout,numeric-method maNsc,marrayLayout-method maNspots<-,marrayLayout,numeric-method maNspots,marrayLayout-method maNsr<-,marrayLayout,numeric-method maNsr,marrayLayout-method maPlate<-,marrayLayout-method maPlate,marrayLayout-method maPrintTip,marrayLayout-method maSpotCol,marrayLayout-method maSpotRow,marrayLayout-method maSub<-,marrayLayout,logical-method maSub<-,marrayLayout,numeric-method maSub,marrayLayout-method print,marrayLayout-method show,marrayLayout-method maPrintTip maGridRow maGridCol maSpotRow maSpotCol
Keywords: classes
Description: Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
URL: ../../../library/marrayClasses/html/marrayLayout-class.html

Entry: marrayNorm-class
Aliases: marrayNorm-class marrayNorm maA maA<- maM maM<- maMloc maMloc<- maMscale maMscale<- [,marrayNorm-method cbind,marrayNorm-method coerce,marrayRaw,marrayNorm-method coerce,marrayNorm,exprSet-method coerce,marrayNorm,marraySpots-method maA<-,marrayNorm,matrix-method maA,marrayNorm-method maControls<-,marrayNorm-method maControls,marrayNorm-method maGnames,marrayNorm-method maGridCol,marrayNorm-method maGridRow,marrayNorm-method maLayout,marrayNorm-method maMloc<-,marrayNorm,matrix-method maMloc,marrayNorm-method maM<-,marrayNorm,matrix-method maM,marrayNorm-method maMscale<-,marrayNorm,matrix-method maMscale,marrayNorm-method maNgc<-,marrayNorm,numeric-method maNgc,marrayNorm-method maNgr<-,marrayNorm,numeric-method maNgr,marrayNorm-method maNormCall,marrayNorm-method maNotes<-,marrayNorm,character-method maNotes,marrayNorm-method maNsamples,marrayNorm-method maNsc<-,marrayNorm,numeric-method maNsc,marrayNorm-method maNspots<-,marrayNorm,numeric-method maNspots,marrayNorm-method maNsr<-,marrayNorm,numeric-method maNsr,marrayNorm-method maPlate<-,marrayNorm-method maPlate,marrayNorm-method maPrintTip,marrayNorm-method maSpotCol,marrayNorm-method maSpotRow,marrayNorm-method maSub<-,marrayNorm-method maSub,marrayNorm-method maTargets,marrayNorm-method maW<-,marrayNorm,matrix-method maW,marrayNorm-method print,marrayNorm-method show,marrayNorm-method maNormCall
Keywords: classes
Description: Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
URL: ../../../library/marrayClasses/html/marrayNorm-class.html

Entry: marrayRaw-class
Aliases: marrayRaw-class marrayRaw maRf maRf<- maGf maGf<- maRb maRb<- maGb maGb<- maW maW<- maLayout maLayout<- [,marrayRaw-method cbind,marrayRaw-method coerce,marrayRaw,exprSet-method coerce,marrayRaw,marraySpots-method maA,marrayRaw-method maControls<-,marrayRaw-method maControls,marrayRaw-method maGb<-,marrayRaw,matrix-method maGb<-,marrayRaw,NULL-method maGb,marrayRaw-method maGf<-,marrayRaw,matrix-method maGf,marrayRaw-method maGnames,marrayRaw-method maGridCol,marrayRaw-method maGridRow,marrayRaw-method maLayout,marrayRaw-method maLG,marrayRaw-method maLR,marrayRaw-method maM,marrayRaw-method maNgc<-,marrayRaw,numeric-method maNgc,marrayRaw-method maNgr<-,marrayRaw,numeric-method maNgr,marrayRaw-method maNotes<-,marrayRaw,character-method maNotes,marrayRaw-method maNsamples,marrayRaw-method maNsc<-,marrayRaw,numeric-method maNsc,marrayRaw-method maNspots<-,marrayRaw,numeric-method maNspots,marrayRaw-method maNsr<-,marrayRaw,numeric-method maNsr,marrayRaw-method maPlate<-,marrayRaw-method maPlate,marrayRaw-method maPrintTip,marrayRaw-method maRb<-,marrayRaw,matrix-method maRb<-,marrayRaw,NULL-method maRb,marrayRaw-method maRf<-,marrayRaw,matrix-method maRf,marrayRaw-method maSpotCol,marrayRaw-method maSpotRow,marrayRaw-method maSub<-,marrayRaw-method maSub,marrayRaw-method maTargets,marrayRaw-method maW<-,marrayRaw,matrix-method maW,marrayRaw-method print,marrayRaw-method show,marrayRaw-method maGnames maGnames<- maTargets maTargets<- maLR maLG maNsamples
Keywords: classes
Description: Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
URL: ../../../library/marrayClasses/html/marrayRaw-class.html

Entry: marraySpots-class
Aliases: marraySpots-class marraySpots [,marraySpots-method maControls<-,marraySpots-method maControls,marraySpots-method maGnames,marraySpots-method maGridCol,marraySpots-method maGridRow,marraySpots-method maLayout,marraySpots-method maNgc<-,marraySpots,numeric-method maNgc,marraySpots-method maNgr<-,marraySpots,numeric-method maNgr,marraySpots-method maNsc<-,marraySpots,numeric-method maNsc,marraySpots-method maNspots<-,marraySpots,numeric-method maNspots,marraySpots-method maNsr<-,marraySpots,numeric-method maNsr,marraySpots-method maPlate<-,marraySpots-method maPlate,marraySpots-method maPrintTip,marraySpots-method maSpotCol,marraySpots-method maSpotRow,marraySpots-method maSub<-,marraySpots-method maSub,marraySpots-method print,marraySpots-method show,marraySpots-method
Keywords: classes
Description: Class "marraySpots", classes and methods for probe sequences spotted on microarrays
URL: ../../../library/marrayClasses/html/marraySpots-class.html

Entry: marrayTwo-class
Aliases: marrayTwo-class marrayTwo maX maX<- maY maY<- [,marrayTwo-method maControls<-,marrayTwo-method maControls,marrayTwo-method maGridCol,marrayTwo-method maGridRow,marrayTwo-method maLayout,marrayTwo-method maNgc<-,marrayTwo,numeric-method maNgc,marrayTwo-method maNgr<-,marrayTwo,numeric-method maNgr,marrayTwo-method maNsamples,marrayTwo-method maNsc<-,marrayTwo,numeric-method maNsc,marrayTwo-method maNspots<-,marrayTwo,numeric-method maNspots,marrayTwo-method maNsr<-,marrayTwo,numeric-method maNsr,marrayTwo-method maPlate<-,marrayTwo-method maPlate,marrayTwo-method maPrintTip,marrayTwo-method maSpotCol,marrayTwo-method maSpotRow,marrayTwo-method maSub<-,marrayTwo-method maSub,marrayTwo-method maTargets,marrayTwo-method maX<-,marrayTwo,matrix-method maX,marrayTwo-method maY<-,marrayTwo,matrix-method maY,marrayTwo-method print,marrayTwo-method show,marrayTwo-method
Keywords: classes
Description: Class "marrayTwo", classes and methods for microarray spot statistics
URL: ../../../library/marrayClasses/html/marrayTwo-class.html

Entry: print-methods
Aliases: print-methods show-methods print
Keywords: methods
Description: Printing methods for microarray objects
URL: ../../../library/marrayClasses/html/print-methods.html

Entry: swirl
Aliases: swirl swirl.1.spot swirl.2.spot swirl.3.spot swirl.4.spot fish.gal SwirlSample.txt SwirlSample
Keywords: datasets
Description: Gene expression data from Swirl zebrafish cDNA microarray experiment
URL: ../../../library/marrayClasses/html/swirl.html
