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/g enomic_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 > > _______________________________________________ > 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

Hello all, Again, I created full Bioconductor annotation libraries for a number of MBNI CustomCDF version 12 chips. URL: http://nugo-r.bioinformatics.nl/NuGO_R.html Entrezg (human, mouse, rat): hgfocushsentrezg hgu133a2hsentrezg hgu133ahsentrezg hgu133bhsentrezg hgu133plus2hsentrezg hgu95av2hsentrezg hgu95bhsentrezg hgu95chsentrezg hgu95dhsentrezg hgu95ehsentrezg huex10stv2hsentrezg hugene10stv1hsentrezg mgu74av2mmentrezg mgu74bv2mmentrezg mgu74cv2mmentrezg moe430ammentrezg moe430bmmentrezg moex10stv1mmentrezg mogene10stv1mmentrezg mouse4302mmentrezg mouse430a2mmentrezg nugohs1a520180hsentrezg nugomm1a520177mmentrezg rae230arnentrezg rae230brnentrezg raex10stv1rnentrezg ragene10stv1rnentrezg rat2302rnentrezg rgu34arnentrezg rgu34brnentrezg rgu34crnentrezg u133x3phsentrezg TAIR (Arabidopsis): ath1121501attairg tilingatsnptilx520433attairg If you need an annotation library that is lacking: just ask! Regards, Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786 F: +31-317-483342 E-mail: Philip.deGroot at wur.nl Internet: http://www.nutrigenomicsconsortium.nl http://humannutrition.wur.nl https://madmax.bioinformatics.nl -----Original Message----- From: Manhong Dai [mailto:daimh@umich.edu] Sent: Thu 30/07/2009 08:38 PM To: bioconductor at stat.math.ethz.ch Subject: [BioC] Custom CDF Version 12 is released Hi, We just release Custom CDF Version 12 officially. All files are available at http://brainarray.mbni.med.umich.ed u/Brainarray/Database/CustomCDF/genomic_curated_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

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 > > > > _______________________________________________ > > 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 > >