[BioC] Problems of CDF environment while doing RMA

Wolfgang Huber wk.huber at gmail.com
Sun Dec 26 12:33:16 CET 2010

Dear Dong

the error message that you get suggests that you verify your internet 
connection - have you done that, and to what result?

The rhesuscdf package is here: 

What version of R/Bioconductor are you using? (Have a look at the 
posting guide, which asks you to provide the output of sessionInfo().)

Also, with statements such as "I also try to install custom CDF file, 
but failed." - try to be more precise. What exactly did you do (report 
it in a way that others can reproduce it), and what exactly happened to 
make you think "it" failed (e.g.: copy/paste the error message)

	Best wishes

Il Dec/26/10 7:56 AM, Shan Dong ha scritto:
> Hello,
> I meet a problem when I doing rma in microarray analysis. The chip name is
> Rhesus<http://www.affymetrix.com/support/technical/byproduct.affx?product=rhesus>
> from
> Macaca_mulatta by Affymetrix.
> My R commands are as follow:
> library(tools)
> library(limma)
> library(Biobase)
> library(affy)
> targets<- readTargets("affy_targets.txt")
> data<- ReadAffy(filenames=targets$FileName)
> eset<- rma(data)
> There is ana error when I doing RMA.
>> eset<- rma(data)
> Error in getCdfInfo(object) :
>    Could not obtain CDF environment, problems encountered:
> Specified environment does not contain Rhesus
> Library - package rhesuscdf not installed
> Bioconductor - could not connect
> I also try to install custom CDF file, but failed.
> Could you help me?
> Thank you very much in advance.
> Best,
> Dong Shan
>> eset<- justGCRMA()
> Computing affinities
> Error in getCDF(cdfpackagename) :
>    The current operation could not access the Bioconductor repository. Please
> check your internet connection, and report further problems to
> bioconductor at stat.math.ethz.ch
> 	[[alternative HTML version deleted]]
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Wolfgang Huber

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