Hello everyone,

I am looking for differential expression of codelink data. I am not sure whether it's achievable by codelink R package. I found something

pdata = read.AnnotatedDataFrame("targets.txt")

codset = readCodelinkSet(filename = pdata$FileName, phenoData = pdata) 

in codelink R package. Is this for differential expression. I could not find any example from codelink package to perform differential expression on codelink data. Any reference link,  example, suggestion is highly appreciated. Thanks

codelink uses the limma package for differential expression analysis, as you will see from Section 6 of the Codelink Introduction:

http://www.bioconductor.org/packages/release/bioc/vignettes/codelink/inst/doc/Codelink_Introduction.pdf

So you now probably need to consult the limma User's Guide:

http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf

The CodelinkSet objects obtained with readCodelinkSet() behave in almost every aspect as an ExpressionSet object (and if they don't please report it in this support site). You can also get a matrix of intensities with exprs(codset). So in principle, any statistical method that uses matrices or ExpressionSet objects could be used for analysis. A particular case highlighted in the codelink vignette (and kindly mentioned by Gordon Smyth in his reply) is the limma package. In the vignette a very brief example is mentioned, but most of the information in the limma user's guide, in particular that referring with single channel microarrays, applies. With that example in mind, please read the limma user's guide, which provides many comprehensive examples on the application of linear models for the analysis of microarray experiments.