Question: Fixing brainarray repository link for mac os x
0
gravatar for Yair Benita
9.9 years ago by
Yair Benita80
Yair Benita80 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? Thanks, Yair
annotation go customcdf cdf gcrma • 443 views
ADD COMMENTlink modified 9.9 years ago by James W. MacDonald51k • written 9.9 years ago by Yair Benita80
Answer: Fixing brainarray repository link for mac os x
0
gravatar for James W. MacDonald
9.9 years ago by
United States
James W. MacDonald51k 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
ADD COMMENTlink written 9.9 years ago by James W. MacDonald51k
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
ADD REPLYlink written 9.9 years ago by Yair Benita80
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