Hello, bioconductor developers: Are there any one working on to make bioconductor able to read affy's 100K and 500K SNP chips? I tried make.cdf.packages() in Suse, it worked on 10K arrays, but failed on later type of arrays. The error info is: bioconductor just can't handle the chip type right now. So can somebody work on that to make it available for public or if not for public right now, can somebody make an R package for me to install the cdf packages of 100K and 500K cdf files on my Suse and/or window machines? Thanks, Jacob This email message, including any attachments, is for the so...{{dropped}}

the oligo and makePlatformDesign packages handle these chips. they are in devel stages (and thus available in the devel section of bioc) so testers are welcomed. On Thu, 27 Oct 2005, Zhang, Jacob wrote: > Hello, bioconductor developers: > > Are there any one working on to make bioconductor able to read affy's > 100K and 500K SNP chips? > > I tried make.cdf.packages() in Suse, it worked on 10K arrays, but failed > on later type of arrays. The error info is: bioconductor just can't > handle the chip type right now. > > So can somebody work on that to make it available for public or if not > for public right now, can somebody make an R package for me to install > the cdf packages of 100K and 500K cdf files on my Suse and/or window > machines? > > Thanks, > > Jacob > > > > This email message, including any attachments, is for the so...{{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Hi Jacob, although the documentation is not ready yet (for this reason you can contact me directly), oligo and makePlatformDesign can handle both 100K and 500K SNP chips (provided that you have the sequence and annotation files). at this point, you need to build the environment using the function: > makePDpackage(CDF_file,probe_fasta_file,annot_file,type="SNP") after installing the package created from the step above, you can read your CEL files using: > data = read.celfiles(list.celfiles()) kind regards, benilton On Thu, 27 Oct 2005, Zhang, Jacob wrote: > Hello, bioconductor developers: > > Are there any one working on to make bioconductor able to read affy's > 100K and 500K SNP chips? > > I tried make.cdf.packages() in Suse, it worked on 10K arrays, but failed > on later type of arrays. The error info is: bioconductor just can't > handle the chip type right now. > > So can somebody work on that to make it available for public or if not > for public right now, can somebody make an R package for me to install > the cdf packages of 100K and 500K cdf files on my Suse and/or window > machines? > > Thanks, > > Jacob > > > > This email message, including any attachments, is for the so...{{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Hi, I'm sure what I want to do is really simple and straight forward, but right now I can't think of how doing it! I work on custom Affymetrix arrays, no MM features. I have a filtered eset object pre-processed by RMA, quantiles normalisation and median polishing summarisation of the probesets. Because the question I'm asking to the experiment is very tedious, I want to make sure that all the probes matching the 5.8s rRNA are calibrated to the same level, even if the amount and quality of starting RNA is different. I tried the affy.scalevalue.exprSet() function but it does scale the whole chips, regardless of the probesets I want to act as controls of the expression level. Can someone please point me out on the right function ? Thank you very much for your time and help, Celine (R2.2.0 & affy 1.8.1) -- Celine Carret PhD Pathogen Microarrays group The Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK. tel. +44 (0)1223 834 244 ext.7123 fax. +44 (0)1223 494 919 email: ckc at sanger.ac.uk http://www.sanger.ac.uk/PostGenomics/PathogenArrays/