Dear BioC list, I would like to create the annotation package for Affymetrix Mouse Diversity Array (MOUSEDIVm520650) and run CNV analysis on these arrays. However I am missing three files, which are required to successfully build the annotation package and run the analysis. splineParamFile crlmmInfoFile referenceDistFile Based on the description in pdInfoBuilder reference manual they are required to run the crlmm function (from the crlmm package). Usually the files are available at the svn repository (described in the pdInfoBuilder reference manual) https://hedgehog.fhcrc.org/bioc-data/trunk/annotation/parms_store I could not access this svn repository (readonly account + password does not work). Could somebody provide me these files? Best regards Robert -- Robert Ivanek Postdoctoral Fellow Schuebeler Group Friedrich Miescher Institute Maulbeerstrasse 66 4058 Basel / Switzerland Office phone: +41 61 697 6100

Hi Robert, I'm sure Benilton will have more to say about this, but the files you are looking for do not exist in the svn repository. What does exist there are files for all the Affy human SNP chips from the 100K and 500K sets to the genomewide.snp5 and genomewide.snp6 chips. Best, Jim Ivanek, Robert wrote: > Dear BioC list, > > I would like to create the annotation package for Affymetrix Mouse > Diversity Array (MOUSEDIVm520650) and run CNV analysis on these arrays. > > However I am missing three files, which are required to successfully > build the annotation package and run the analysis. > > splineParamFile > crlmmInfoFile > referenceDistFile > > Based on the description in pdInfoBuilder reference manual they are > required to run the crlmm function (from the crlmm package). > Usually the files are available at the svn repository (described in the > pdInfoBuilder reference manual) > https://hedgehog.fhcrc.org/bioc-data/trunk/annotation/parms_store > I could not access this svn repository (readonly account + password does > not work). Could somebody provide me these files? > > Best regards > > Robert > > -- 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

Dear Robert, the story is a bit more complicated than that. But to be objective, here's the summary: The information used by the crlmm package requires you to have a training dataset (on the human case, we use HapMap). With this reference set, we estimate a number of parameters that go into annotation package. Then, once the annotation package is created, you'll be able to run crlmm on the dataset you refer to. Because this is not a trivial task, I'm happy to discuss with you (off-list) some further details. b On 27 May 2010 13:53, Ivanek, Robert <robert.ivanek at="" fmi.ch=""> wrote: > Dear BioC list, > > I would like to create the annotation package for Affymetrix Mouse > Diversity Array (MOUSEDIVm520650) and run CNV analysis on these arrays. > > However I am missing three files, which are required to successfully > build the annotation package and run the analysis. > > splineParamFile > crlmmInfoFile > referenceDistFile > > Based on the description in pdInfoBuilder reference manual they are > required to run the crlmm function (from the crlmm package). > Usually the files are available at the svn repository (described in the > pdInfoBuilder reference manual) > https://hedgehog.fhcrc.org/bioc-data/trunk/annotation/parms_store > I could not access this svn repository (readonly account + password does > not work). Could somebody provide me these files? > > Best regards > > Robert > > > -- > Robert Ivanek > Postdoctoral Fellow Schuebeler Group > Friedrich Miescher Institute > Maulbeerstrasse 66 > 4058 Basel / Switzerland > Office phone: +41 61 697 6100 > > _______________________________________________ > 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 >