Hello, The Drosophila chip CDF file package is missing from the CDF data page at: http://www.bioconductor.org/data/cdfenvs/cdfenvs.html All of the other chips that we are using are there. Is the package for this chip in a special place? Do you need a copy of the original Affy CDF file for this chip? Finally, since I have the CDF file but not a prepared package, is there a way for me to use the newest version of the R affy library with the CDF file directly? We are having lots of fun with the bioconductor tools! Thanks! -- Terry ***************************************** ***************************************** TERRY GAASTERLAND Associate Professor and Head Laboratory of Computational Genomics The Rockefeller University 1230 York Avenue, New York, NY 10021-6399 ph 212-327-7755 cell 646-207-4600 fax -7765 lab -7785/7778/7779 email gaasterland@rockefeller.edu url http://genomes.rockefeller.edu Assistant: Nancy Sosa 212-327-7756 ***************************************** *****************************************

>>>>> "terry" == Terry Gaasterland <gaasterland@rockefeller.edu> writes: terry> Hello, terry> The Drosophila chip CDF file package is missing from the CDF terry> data page at: terry> http://www.bioconductor.org/data/cdfenvs/cdfenvs.html terry> All of the other chips that we are using are there. Is the terry> package for this chip in a special place? terry> Do you need a copy of the original Affy CDF file for this chip? terry> Finally, since I have the CDF file but not a prepared package, terry> is there a way for me to use the newest version of the R affy terry> library with the CDF file directly? terry> We are having lots of fun with the bioconductor tools! You can have more fun, now. See: http://www.bioconductor.org/repository/devel/package/html/makecdfenv.h tml for the tool used to make the datapackages! best, -tony -- A.J. Rossini Rsrch. Asst. Prof. of Biostatistics U. of Washington Biostatistics rossini@u.washington.edu FHCRC/SCHARP/HIV Vaccine Trials Net rossini@scharp.org -------------- http://software.biostat.washington.edu/ ---------------- FHCRC: M: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email UW: Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX (my tuesday/wednesday/friday locations are completely unpredictable.)

On Mon, Dec 09, 2002 at 04:19:56PM -0500, Terry Gaasterland wrote: > > Hello, > > The Drosophila chip CDF file package is missing from the CDF > data page at: > > http://www.bioconductor.org/data/cdfenvs/cdfenvs.html > > All of the other chips that we are using are there. Is the > package for this chip in a special place? > nop. everything we have in the shop is there I think. > Do you need a copy of the original Affy CDF file for this chip? yep. So we can add it to the collection. > > Finally, since I have the CDF file but not a prepared package, > is there a way for me to use the newest version of the R affy > library with the CDF file directly? You can do that too. Here we go: a) one way (*should* work... non tested): library(affy) ## read your CEL data in 'myAffyBatch' myname <- myAffyBatch@cdfName ## end R session ## have the CDF file named like <myname>.CDF ## and move it (or make a link) to your working directory with R ## start R again. You should not have to worry about the cdf environment b) a another way: library(affy) ## read your CEL data in 'myAffyBatch' mycdf <- read.cdffile("path/to/my/file.CDF") mylocationsenv <- getLocationsData.Cdf(mycdf, want.na=FALSE) env.name <- myAffyBatch@cdfName assignenv.name, mylocationsenv) ## then you can proceed without worrying about the cdf stuff... Hopin' it helps, L. > > We are having lots of fun with the bioconductor tools! > > Thanks! > > -- Terry > > > ***************************************** > ***************************************** > TERRY GAASTERLAND > Associate Professor and Head > Laboratory of Computational Genomics > The Rockefeller University > 1230 York Avenue, New York, NY 10021-6399 > > ph 212-327-7755 cell 646-207-4600 > fax -7765 > lab -7785/7778/7779 > email gaasterland@rockefeller.edu > url http://genomes.rockefeller.edu > > Assistant: Nancy Sosa 212-327-7756 > ***************************************** > ***************************************** > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent