[BioC] gcrma with hgu133a and hgu133a2

[James W. MacDonald]

Hi Max,

Max Kauer wrote:
> Hi 
> 
> I combined two affybatches (hgu113a and hgu133a2) with the matchprobes package.  With the combined affybatch I could run rma. Now I would also like to run gcrma for which I would need a "hgu133aa2probe" package. 
> Can I make probe package from the new cdf file? Or could I simply subset the hgu133aprobe package with the probesets from the new cdf environment?

You will need another package called hgu133aa2probe. You also want to 
call your newcdf 'hgu133aa2' without the cdf at the end. Note the error 
where R can't find hgu133aa2cdfcdf below.

You might be able to simply take the hgu133a2probe package and rename 
and install as hgu133aa2. But then maybe not -- I have never tried it, 
and I don't know offhand what all you will need to rename. Certainly the 
package itself, and parts of the DESCRIPTION file.

An alternative is to get the hgu133a2_probe_tab file from affy and 
subset it to only contain the probesets that are in your new cdf. Then 
build the probe package using makeProbePackage() in matchprobes. Either 
way, you will need to be able to install the package, so if  you are on 
Windows you will also need to get set up to install packages. See the R 
Windows FAQ, specifically 7.1.

Best,

Jim


> 
> Thanks for your help!
> Max
> 
> Here's what I did:
> comBatch <- combineAffyBatch(list(Data.a, Data.a2), c("hgu133aprobe", "hgu133a2probe"), newcdf = "hgu133aa2cdf") 
> comAffyBatch <- comBatch$dat
> hgu133aa2cdf <- comBatch$cdf
> 
> eset <- gcrma(comBatch)
> Adjusting for optical effect............................Done.
> Computing affinities[1] "Checking to see if your internet connection works..."
> [1] "Environment hgu133aa2cdfcdf was not found in the Bioconductor repository."
> [1] "Checking to see if your internet connection works..."
> [1] "Environment hgu133aa2cdfprobe was not found in the Bioconductor repository."
> Error in get(probepackagename) : 
>   variable "hgu133aa2cdfprobe" was not found
> --
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623