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 >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > 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 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues