bioconductor-request at stat.math.ethz.ch wrote: > Send Bioconductor mailing list submissions to > bioconductor at stat.math.ethz.ch > > To subscribe or unsubscribe via the World Wide Web, visit > https://stat.ethz.ch/mailman/listinfo/bioconductor > or, via email, send a message with subject or body 'help' to > bioconductor-request at stat.math.ethz.ch > > You can reach the person managing the list at > bioconductor-owner at stat.math.ethz.ch > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Bioconductor digest..." > > > Today's Topics: > > 1. Re: crlmm warning (Morten Mattingsdal) > 2. Re: crlmm warning (James W. MacDonald) > 3. Re: crlmm warning (Benilton Carvalho) > 4. Re: crlmm warning (Morten Mattingsdal) > 5. Re: Unable to compile the impute package on debian with gcc > 4.1 (Seth Falcon) > 6. Re: rma on new samples (Hassane, Duane) > 7. Re: crlmm warning (Benilton Carvalho) > 8. NEwbie: How to determine significant enrichment differences > of GO term vectors? (Johannes Graumann) > 9. Re: rma on new samples (Kuhn, Max) > 10. Options for spatial normalization? (Oliver Homann) > 11. how to enlarge memory (Yihuan Xu) > 12. Re: how to enlarge memory (James W. MacDonald) > 13. Re: Options for spatial normalization? (Jay Konieczka) > 14. RMA, RefRMA questions (James Anderson) > 15. Re: RMA, RefRMA questions (Kuhn, Max) > 16. Re: RMA, RefRMA questions (James W. MacDonald) > 17. Re: RMA, RefRMA questions (Kuhn, Max) > 18. two questions about limma (cont.2) (De-Jian,ZHAO) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 07 Mar 2007 13:10:59 +0100 > From: Morten Mattingsdal <mortenm at="" inbox.com=""> > Subject: Re: [BioC] crlmm warning > To: Morten Mattingsdal <mortenm at="" inbox.com=""> > Cc: BioC <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <45EEABD3.70208 at inbox.com> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hello again, > Ill just answer that myself, since I posted a bit too prematurely. > Seems like I need to use the makePlatformDesign package, with the code: > > > library(makePlatformDesign) > > > makePDpackage("Mapping50K_Xba240.CDF","Mapping50K_Xba240_probe_fasta ","Mapping50K_Xba240_annot.csv",type="SNP") > > R CMD INSTALL pdmapping50kxba240 > > I find it ... non-trivial.. to locate the fasta file for Nsp and Sty > arrays, but I think Ill harass Affyemtrix Inc for that. > > I am aware that the oligo package is in development, but It would be > nice to have some vignettes to read > > regards > morten > > > > > Morten Mattingsdal wrote: > >> Hello everyone, >> >> Ive managed to get the oligo package and the crlmm function up and >> running. Ive also installed the meta-data libraries from this URL >> http://www.biostat.jhsph.edu/~bcarvalh/oligoAddOns.tar.gz >> provided by Benliton >> >> but when I run the commands: >> >> >files <- list.celfiles() >> >snpFSet <- read.celfiles(files) >> > >> >Welcome to the pd.Mapping250K_Nsp prototype pdInfo package >> >WARNING: DO NOT USE THIS PACKAGE FOR ANY ANALYSIS. >> >THIS PACKAGE IS FOR INTERFACE PROTOTYPE USE ONLY! >> >THE DATA HAS NOT BEEN VALIDATED AND LIKELY HAS ERRORS. >> >Have fun! >> >> Im am happy that this information is warning me, but to my point: >> - When will the "safe" mapping libraries come? >> - Can I build this by myself ? >> >> I want to compare brlmm from Affymetrix and crlmm from BioC genotype >> calls for my data >> >> regards >> morten >> >> _______________________________________________ >> 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 >> >> >> . >> >> >> > > > > ------------------------------ > > Message: 2 > Date: Wed, 07 Mar 2007 08:49:07 -0500 > From: "James W. MacDonald" <jmacdon at="" med.umich.edu=""> > Subject: Re: [BioC] crlmm warning > To: Morten Mattingsdal <mortenm at="" inbox.com=""> > Cc: BioC <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <45EEC2D3.6000504 at med.umich.edu> > Content-Type: text/plain; charset="utf-8"; format=flowed > > Morten Mattingsdal wrote: > > >> I find it ... non-trivial.. to locate the fasta file for Nsp and Sty >> arrays, but I think Ill harass Affyemtrix Inc for that. >> >> > > These files are available on the support page for the 500K snp arrays > (near the bottom). > > http://www.affymetrix.com/support/technical/byproduct.affx?product=5 00k > >