# Manipulation of Codelink Bioarrays data.

## Documentation for package ‘codelink’ version 1.8.1

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

arrayNew | Create a new x11 device
arraySize | Determine the size of the array
as.matrix.Codelink | Return a matrix of intensity values
bkgdCorrect | Background correction of intensity values.
Codelink-class | Class Codelink
codelink.example | Dataset of class 'Codelink'
codelink.exprset | Dataset of class 'CodelinkSet'
createWeights | 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.
fc2Cond | Select probes based on fold change calculation
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 objects.
normalize.loess | Normalized chips using cyclic loess.
plotCorrelation | Plot correlation scatterplot between two arrays
plotCV | Plot of CV
plotDensities | Plot Densities
plotDensities,Codelink-method | Plot Densities
plotMA | MA plot
printHead | Print briefly a Codelink object
readCodelink | 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,Codelink-method | Class Codelink
SNR | Calculate SNR
writeCodelink | Write a Codelink object to file.
[,Codelink-method | Class Codelink