[BioC] Fixing brainarray repository link for mac os x

[James W. MacDonald]

Hi Yair,

Yair Benita wrote:
> Hi All,
> I am a fan of the brainarray customCDF and now routinely normalize my Affy
> files with these CDFs. I find the annotation much more reliable than Affy's.
> I typically use GCRMA after reading the CEL files.
> On the mac I install these customCDFs manually from source. GCRMA has the
> ability to fetch the CDFs when it cannot find them. However, it gives the
> same error that the brainarray repository cannot be found. I wonder if we
> can fix it somehow. I can't find the location where gcrma stores this link.
> Ideally I would like it to go to the correct link (
> http://brainarray.mbni.med.umich.edu/bioc/) and install the customCDFs from
> source. Is there a way to do this?

It's not the gcrma package that does this, but the affy package. Anyway, 
the behavior of this functionality is dependent on whatever you have in

options("pkgType")

and if the option you have there is "mac.binary", then there will be 
problems as there are no binary mac packages available. Since creating 
mac binaries can be a bit of a pain, I wouldn't expect them to be 
forthcoming any time soon. In addition, much of the functionality is 
hard-coded (and for everything but brainarray cdfs works as is), so I 
don't see it changing on our side either.

Since you have the ability to install from source, you could get 
auto-installation by changing the pkgType variable to "source", after 
which the auto-install should work.

Best,

Jim


> 
> Thanks,
> Yair
> 
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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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