[BioC] Custom CDF Version 12 is released

[Manhong Dai]

Hi Yair,


	Thanks a lot for telling me this glitch. I temporarily disabled Mac
Repository. 


	It seems that I better stop supporting Mac Binary version because I
actually don't have a Mac machine to test them. Mac users can install it
from source packages anyway. I will ask for suggestion from BioConductor
developer.


Best,
Manhong
On Fri, 2009-07-31 at 23:32 -0400, Yair Benita wrote:
> Dear Manhong,
> I would just like to note here my own experience installing v12 on R 2.9.1
> on MacosX.
> Using the R package installer I selected "Other Repository" and used the
> URL: http://brainarray.mbni.med.umich.edu/bioc/
> Next I installed several custom CDF files in binary format and got the
> following error for every cdf I tried:
> 
> Error in function (package, help, pos = 2, lib.loc = NULL, character.only =
> FALSE,  : 'hgu95av2hsentrezgcdf' is not a valid installed package
> 
> For a while I could not figure this problem, but then I re-installed the
> custom CDF from source (by simply un-checking "Binary Format Package") and
> it started working fine. I am not sure what is wrong with the binary format
> but hope it will save others some time. I am running on a Quad MacPro.
> 
> Thanks,
> Yair
> 
> on 7/30/09 2:38 PM, Manhong Dai at daimh at umich.edu wrote:
> 
> > Hi,
> > 
> > 
> > We just release Custom CDF Version 12 officially.
> > 
> > 
> > All files are available at
> > http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_cur
> > ated_CDF.asp. All R packages are also in our own R repository. You should be
> > able to use biocLite() to install them, just like other bioconductor packages.
> > 
> > 
> > As a reminder, almost all Affymetrix chips are supported in Custom CDF. You
> > can even use traditional method (ReadAffy and rma) to analyze latest gene
> > chips, such as HuGene10stv1, HTHGU133PlusPM, etc.
> > 
> > 
> > We also updated probeset web application that has all probe's genome location,
> > user can input whatever probeset name to get sequence, chromosome and
> > location. It is at http://arrayanalysis.mbni.med.umich.edu/probeset/.
> > 
> > 
> > In addition, We released a R library 'CustomCDF' at
> > http://arrayanalysis.mbni.med.umich.edu/MBNIUM.html#CustomCDF. The library has
> > a few useful tools, such as retrieving probes that have a hit with snp, and
> > removing them from cdf library on-the-fly, etc.
> > 
> > 
> > By the way, our public WGAS is still using Custom CDF version 11, it should be
> > updated in a few weeks.
> > 
> > 
> > We want to thank Dr. De Bondt, An at Johnson & Johnson for finding a bug
> > during preview.
> >  
> > 
> > Best,
> > Manhong Dai
> > The Molecular & Behavioral Neuroscience Institute (MBNI)
> > University of Michigan
> > 
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>