# Manipulation of Codelink Bioarrays data.

## Documentation for package ‘codelink’ version 1.30.9

- 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