Manipulation of Codelink microarray data


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Documentation for package ‘codelink’ version 1.64.0

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arrayNew Create a new x11 device
arraySize Determine the size of the array
as.matrix.Codelink Return a matrix of intensity values
averageProbes averageProbes
averageProbes-method averageProbes
bkgdCorrect Background correction of intensity values.
class::CodelinkSet Class CodelinkSet
class::CodelinkSetUnique Class CodelinkSetUnique
class:Codelink Class Codelink
codCorrect Background correction of intensity values.
codCorrect-method Background correction of intensity values.
Codelink Class Codelink
Codelink-class Class Codelink
codelink.example Dataset of class 'Codelink'
Codelink2CodelinkSet Class CodelinkSet
CodelinkSet Class CodelinkSet
CodelinkSet-class Class CodelinkSet
CodelinkSetUnique Class CodelinkSetUnique
CodelinkSetUnique-class Class CodelinkSetUnique
codNormalize Normalization wrapper for Codelink/CodelinkSet objects.
codNormalize-method Normalization wrapper for Codelink/CodelinkSet objects.
codPlot Diagnostic plots for CodelinkSet object.
codPlot-method Diagnostic plots for CodelinkSet object.
codPreprocess Class CodelinkSet
codPreprocess-method Class CodelinkSet
codset Dataset of class 'CodelinkSet'
createWeights Create weight for Codelink chips
createWeights-method Create weight for Codelink chips
cutCV Calculate cutoff based in CV.
decDetect Determine decimal type of Codelink files
dim.Codelink Return the dimension of a Codelink object.
exprs-method Class CodelinkSet
fc2Cond Select probes based on fold change calculation
getBkg Class CodelinkSet
getBkg-method Class CodelinkSet
getFlag Class CodelinkSet
getFlag-method Class CodelinkSet
getInfo Class CodelinkSet
getInfo-method Class CodelinkSet
getInt Class CodelinkSet
getInt-method Class CodelinkSet
getSNR Class CodelinkSet
getSNR-method Class CodelinkSet
getWeight Class CodelinkSet
getWeight-method Class CodelinkSet
imageCodelink Image plot of Codelink arrays
logCodelink Application of logCodelink to Codelink object
mergeArray Merge Codelink Bioarrays Data
na2false Set NAs to FALSE
normalize Normalization wrapper for Codelink/CodelinkSet objects.
normalize-method Normalization wrapper for Codelink/CodelinkSet objects.
plotCorrelation Plot correlation scatterplot between two arrays
plotCV Plot of CV
plotDensities Plot Densities
plotDensities-method Plot Densities
plotMA MA plot
printHead Print briefly a Codelink object
probeNames Class CodelinkSet
probeNames-method Class CodelinkSet
probeTypes Class CodelinkSet
probeTypes-method Class CodelinkSet
readCodelink Read Codelink Bioarrays Data
readCodelinkSet Read Codelink Bioarrays Data
readHeader Read Header from Codelink Bioarrays Files
readHeaderXLS Read Header from XLS exported Codelink Bioarrays Files
reportCodelink Write a report of genes selected in HTML
selCV Select based on CV cutoff.
show-method Class Codelink
SNR Calculate SNR
writeCodelink Write a Codelink object to file.
writeCodelink-method Write a Codelink object to file.
[-method Class Codelink