[BioC] Problem using justGCRMA

[James W. MacDonald]

Hi Omar,

On 5/5/2011 7:01 AM, Omar Gutierrez Arenas wrote:
> Dear Colleagues,
>
> I'm using redefined cdf from GATExplorer to analyse microarray data. They
> work OK with rma, but they don't with gcrma. Does this have an easy
> solution? Bellow you can see commands and messages.

Please don't hijack existing threads. If you have a new question, send a 
new email.

As for the solution, you could ask the GATExplorer people to create the 
required probe packages. Or you could use the MBNI remapped cdf 
packages, which have corresponding probe packages.

Best,

Jim


>
>> dtst<- ReadAffy()
>
>> dtst at cdfName<- "genemappermouse4302"
>
>> pdtst<- gcrma(dtst)
> Adjusting for optical effect......Done.
> Computing affinities[1] "Checking to see if your internet connection
> works..."
> [1] "Environment genemappermouse4302probe was not found in the Bioconductor
> repository."
> Error in get(probepackagename) :
>    object 'genemappermouse4302probe' not found
>
>> affinfo<- compute.affinities("genemappermouse4302")
> Computing affinities[1] "Checking to see if your internet connection
> works..."
> [1] "Environment genemappermouse4302probe was not found in the Bioconductor
> repository."
> Error in get(probepackagename) :
>    object 'genemappermouse4302probe' not found
>
>> pdtst<- rma(dtst)
> Background correcting
> Normalizing
> Calculating Expression
>>
>
> Looking forward,
>
> Omar
>
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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