Manipulation of Codelink microarray data

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Documentation for package ‘codelink’ version 1.77.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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