[BioC] Fixing brainarray repository link for mac os x

[Yair Benita]

Hi James,
Thanks a lot - this works great.
The reason I had issues with it is that installing manually at system level did not work. When running gcrma, it kept trying to download the files. When I installed manually at user level it started working. Setting the options("pkgType") to source works great and I don't have to worry about getting all the files prior to normalization.
Thanks again.
Yair

On Dec 14, 2009, at 5:22 PM, James W. MacDonald wrote:

> 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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> 
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> James W. MacDonald, M.S.
> Biostatistician
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