Question: Differential expression on codelink data
1
gravatar for Agaz Hussain Wani
4.3 years ago by
India
Agaz Hussain Wani260 wrote:

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

ADD COMMENTlink modified 4.3 years ago by Diego Diez730 • written 4.3 years ago by Agaz Hussain Wani260
Answer: Differential expression on codelink data
2
gravatar for Gordon Smyth
4.3 years ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:

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

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Gordon Smyth38k

Thanks Gordon Smyth for your comments. I will go through your limma package to know more.

ADD REPLYlink written 4.3 years ago by Agaz Hussain Wani260
Answer: Differential expression on codelink data
1
gravatar for Diego Diez
4.3 years ago by
Diego Diez730
Japan
Diego Diez730 wrote:

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.

ADD COMMENTlink written 4.3 years ago by Diego Diez730

Thanks Diego Diez ,please consider to add some more explanation about differential expression in your codelink package.

ADD REPLYlink written 4.3 years ago by Agaz Hussain Wani260
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