[BioC] globaltest on cDNA

[Oosting, J. (PATH)]

I don't think the vignette will help you very far in this case. You
haven't provided enough information to help you completely but I can
sketch you a scenario.

Ideally you will need an (Biobase) exprSet object with intensity data
for both channels to perform the globaltest

Read in your samples with limma and do proper normalizations. (read
limma vignette on how to do this)
You now have a MAList object, convert this with RG.MA() to an RGList
object
This object can be converted to an exprSet object using the convert
package
Eset<-as(RG,"exprSet")

If you have 5 slides you can now perform a globaltest between the
treated and controls with a command like this

globaltest(Eset,c(1,0,1,0,1,0,1,0,1,0))


Jan Oosting


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Lang Chen
Sent: dinsdag 14 maart 2006 0:45
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] globaltest on cDNA

Dear all,

 

I have cDNA chips( treatmean(cys5)/control(cys3)) and want to run
globaltest. Could anyone show me how to do this in the package of
globaltest?

 

Thank you for your help.

 

Lang Chen

Biostatistics

Univ of Alabama at Birmingham

 


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