Entry: Codelink-class
Aliases: Codelink-class [,Codelink-method show,Codelink-method
Keywords: classes
Description: Class Codelink
URL: ../../../library/codelink/html/Codelink-class.html

Entry: Nondocumented-objects
Aliases: Nondocumented-objects class::CodelinkSet CodelinkSet CodelinkSet-class codCorrect codNormalize codPreprocess getBkg getInt getInfo getSNR getType probeNames probeTypes meanSNR codPlot normalize.median chipDevice filterSNR codUniverse writeCluster filterSNR,matrix-method codPlot,MArrayLM-method writeCluster,MArrayLM-method codPlot,Codelink-method filterSNR,Codelink-method codUniverse,Codelink-method writeCluster,Codelink-method codCorrect,CodelinkSet-method codNormalize,CodelinkSet-method codPreprocess,CodelinkSet-method getBkg,CodelinkSet-method getInt,CodelinkSet-method getInfo,CodelinkSet-method getSNR,CodelinkSet-method probeNames,CodelinkSet-method probeTypes,CodelinkSet-method meanSNR,CodelinkSet-method codPlot,CodelinkSet-method exprs,CodelinkSet-method chipDevice,CodelinkSet-method filterSNR,CodelinkSet-method codUniverse,CodelinkSet-method writeCluster,CodelinkSet-method readCodelink2 readCodelinkFiles Codelink2eSet eSet2Codelink guessAnnotation summary,Codelink-method summaryFlag summaryFlag,Codelink-method summaryFlag,matrix-method
Keywords: documentation internal
Description: Here goes every undocumented function.
URL: ../../../library/codelink/html/Nondocumented-objects.html

Entry: SNR
Aliases: SNR
Keywords: documentation utilities
Description: Calculate SNR
URL: ../../../library/codelink/html/SNR.html

Entry: arrayNew
Aliases: arrayNew
Keywords: documentation utilities
Description: Create a new x11 device
URL: ../../../library/codelink/html/arrayNew.html

Entry: arraySize
Aliases: arraySize
Keywords: documentation utilities
Description: Determine the size of the array
URL: ../../../library/codelink/html/arraySize.html

Entry: as.matrix.Codelink
Aliases: as.matrix.Codelink
Keywords: documentation utilities
Description: Return a matrix of intensity values
URL: ../../../library/codelink/html/as.matrix.Codelink.html

Entry: bkgdCorrect
Aliases: bkgdCorrect
Keywords: documentation utilities
Description: Background correction of intensity values.
URL: ../../../library/codelink/html/bkgdCorrect.html

Entry: codelink.example
Aliases: codelink.example
Keywords: datasets
Description: Dataset of class 'Codelink'
URL: ../../../library/codelink/html/codelink.example.html

Entry: createWeights
Aliases: createWeights
Keywords: documentation utilities
Description: Create weight for Codelink chips
URL: ../../../library/codelink/html/createWeights.html

Entry: cutCV
Aliases: cutCV
Keywords: documentation utilities
Description: Calculate cutoff based in CV.
URL: ../../../library/codelink/html/cutCV.html

Entry: decDetect
Aliases: decDetect
Keywords: documentation utilities
Description: Determine decimal type of Codelink files
URL: ../../../library/codelink/html/decDetect.html

Entry: dim.Codelink
Aliases: dim.Codelink
Keywords: documentation utilities
Description: Return the dimension of a Codelink object.
URL: ../../../library/codelink/html/dim.Codelink.html

Entry: fc2Cond
Aliases: fc2Cond
Keywords: documentation utilities
Description: Select probes based on fold change calculation
URL: ../../../library/codelink/html/fc2Cond.html

Entry: imageCodelink
Aliases: imageCodelink
Keywords: documentation utilities
Description: Image plot of Codelink arrays
URL: ../../../library/codelink/html/imageCodelink.html

Entry: logCodelink
Aliases: logCodelink
Keywords: documentation utilities
Description: Application of logCodelink to Codelink object
URL: ../../../library/codelink/html/logCodelink.html

Entry: mergeArray
Aliases: mergeArray
Keywords: documentation utilities
Description: Merge Codelink Bioarrays Data
URL: ../../../library/codelink/html/mergeArray.html

Entry: na2false
Aliases: na2false
Keywords: documentation utilities
Description: Set NAs to FALSE
URL: ../../../library/codelink/html/na2false.html

Entry: normalize
Aliases: normalize
Keywords: documentation utilities
Description: Normalization wrapper for Codelink objects.
URL: ../../../library/codelink/html/normalize.html

Entry: normalize.loess
Aliases: normalize.loess
Keywords: documentation utilities
Description: Normalized chips using cyclic loess.
URL: ../../../library/codelink/html/normalize.loess.html

Entry: plotCV
Aliases: plotCV
Keywords: documentation utilities
Description: Plot of CV
URL: ../../../library/codelink/html/plotCV.html

Entry: plotCorrelation
Aliases: plotCorrelation
Keywords: documentation utilities
Description: Plot correlation scatterplot between two arrays
URL: ../../../library/codelink/html/plotCorrelation.html

Entry: plotDensities
Aliases: plotDensities plotDensities,Codelink-method
Keywords: documentation utilities
Description: Plot Densities
URL: ../../../library/codelink/html/plotDensities.html

Entry: plotMA
Aliases: plotMA
Keywords: documentation utilities
Description: MA plot
URL: ../../../library/codelink/html/plotMA.html

Entry: printHead
Aliases: printHead
Keywords: documentation utilities
Description: Print briefly a Codelink object
URL: ../../../library/codelink/html/printHead.html

Entry: readCodelink
Aliases: readCodelink
Keywords: documentation utilities
Description: Read Codelink Bioarrays Data
URL: ../../../library/codelink/html/readCodelink.html

Entry: readHeader
Aliases: readHeader
Keywords: documentation utilities
Description: Read Header from Codelink Bioarrays Files
URL: ../../../library/codelink/html/readHeader.html

Entry: readHeaderXLS
Aliases: readHeaderXLS
Keywords: documentation utilities
Description: Read Header from XLS exported Codelink Bioarrays Files
URL: ../../../library/codelink/html/readHeaderXLS.html

Entry: reportCodelink
Aliases: reportCodelink
Keywords: documentation utilities
Description: Write a report of genes selected in HTML
URL: ../../../library/codelink/html/reportCodelink.html

Entry: selCV
Aliases: selCV
Keywords: documentation utilities
Description: Select based on CV cutoff.
URL: ../../../library/codelink/html/selCV.html

Entry: writeCodelink
Aliases: writeCodelink
Keywords: documentation utilities
Description: Write a Codelink object to file.
URL: ../../../library/codelink/html/writeCodelink.html
