[BioC] Xlaevis probe sequence file for gcRMA not found.

James W. MacDonald jmacdon at med.umich.edu
Thu Mar 4 19:31:14 CET 2010

Hi Asurain,

Naoki Irie wrote:
> hello there,
> As R could not find "xlaevis2probe" in Bioconductor repository, I could not 
> finish my Affymetrix GeneChip analysis by gcRMA.
> The file does not seem to exist neither on the repository, nor the bioconductor.org website.
> But the original affymetrix probe sequence file itself was available from affymetrix website.
> Does anyone know how to make the Probe sequence data for microarrays of type xenopuslaevis 2 ?

This was an oversight on my part, and the package will be included in 
the next release of Bioconductor (coming up in 8 weeks or so).

To build a probe package yourself, you use the tab-delimited probe file 
from Affymetrix along with the makeProbePackage() function from 
AnnotationDbi. This will create a folder in your current working 
directory that can be built and installed using the R package building 
system (R CMD build and R CMD INSTALL).

If you are on linux, you should be able to do these things by default. 
If on Windows, you will need to get the Rtools toolset that Duncan 
Murdoch makes available on his page:


If on MacOS, you will need to get the Xcode toolset and the GNU Fortran 
compiler from this page:


I have sent you the source and Windows binary offline, so hopefully 
either of those will work for you. If you are on a Mac, then you will 
first need to get the tools from above.



> Thank you
> Asurain
> error message was as follows:
> [1] "Environment xlaevis2probe was not found in the Bioconductor repository."
> Error in  get(probepackagename) : 
>    variable 'xlaevis2probe' was not found.
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
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