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On Dec 5, 2005, at 11:24 AM, Stephen Henderson wrote: > > Hello > I am interested to hear if anyone has had experience of using > custom PM only chips (Affymetrix-for expression) together with > Bioconductor? > > In particular I'd like to know if there are any special > arrangements needed for the CDF file (formatting changes etc) or if > this works seemlessly with the affy Packages for instance? > > I don't foresee any problems but thought it would be prudent to ask > on this forum to avoid unpleasant surprises. I have no practical experience, but there should really be no problem as long as you avoid routines which requires MM probes (like GCRMA and Mas5). You may have problems constructing the cdf environment using the stuff in the makecdfenv package. As I recall, the code explicitely tries to find the the two probes in a probepair. If you use that package make sure that you check what you get. You should at least be able to parse the file using the affxparser package and then you will need to do some post-processing to actually construct the cdf env. I do not mind helping with this, if I can get a copy of the cdf file. It would be nice to have this functionality out of the box in affxparser. Kasper Daniel Hansen > Stephen Henderson > > ********************************************************************** > This email and any files transmitted with it are confidentia... > {{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor

Hi Stephen, I have been working with PM-only custom Affy chips for few years now and working with R has never been a problem. You need to create a special environment or package using your CDF, and some of the affy function will not be available to you, but it isn't so much of a big deal. Best wishes Celine Stephen Henderson wrote: > >Hello >I am interested to hear if anyone has had experience of using custom PM only chips (Affymetrix-for expression) together with Bioconductor? > >In particular I'd like to know if there are any special arrangements needed for the CDF file (formatting changes etc) or if this works seemlessly with the affy Packages for instance? > >I don't foresee any problems but thought it would be prudent to ask on this forum to avoid unpleasant surprises. > >Stephen Henderson > >********************************************************************* * >This email and any files transmitted with it are confidentia...{{dropped}} > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > > > -- 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/

Hi That sounds fine-- and thanks for the re-assurance. When you say some functions will not be available do you simply mean normalizations or summaries using MM probes or other unforeseen consequences? Stephen Henderson Wolfson Inst. for Biomedical Research Cruciform Bldg., Gower Street University College London United Kingdom, WC1E 6BT +44 (0)207 679 6827 -----Original Message----- From: Celine Carret [mailto:ckc@sanger.ac.uk] Sent: 06 December 2005 09:39 To: Stephen Henderson Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] custom PM only chips and CDF files Hi Stephen, I have been working with PM-only custom Affy chips for few years now and working with R has never been a problem. You need to create a special environment or package using your CDF, and some of the affy function will not be available to you, but it isn't so much of a big deal. Best wishes Celine Stephen Henderson wrote: > >Hello >I am interested to hear if anyone has had experience of using custom PM only chips (Affymetrix-for expression) together with Bioconductor? > >In particular I'd like to know if there are any special arrangements needed for the CDF file (formatting changes etc) or if this works seemlessly with the affy Packages for instance? > >I don't foresee any problems but thought it would be prudent to ask on this forum to avoid unpleasant surprises. > >Stephen Henderson > >********************************************************************* * >This email and any files transmitted with it are confidentia...{{dropped}} > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > > > -- 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/ ********************************************************************** This email and any files transmitted with it are confidentia...{{dropped}}