>Ruppert, > >I think you need to give more information before anybody can help. When >you say custom CDF, does this mean you are using the altcdfenv package, >or are you somehow modifying the CDF by hand? Hello Jim, Thank you for the reply. Basically I am trying to create a new CDF which has mixture probes from U95ver2a and U133ver2.0. On the Affy site they don't have this so I have to create it myself. I am not sure what is the best way to do this and on what platform. I tried to find a primer or information on how to create custom made CDF but they don't tell you what the structure of the CDF file should be. Also the other issue is I am using R 2.1.1 on Windows but in the manual they say if you are using Windows then you have to do more to creat and upload the CDF environment. Basically I got the CDF file in ASCII format and now trying to create a CDF package that I can use to analyse chips which are mixture of U133 and U95 (not good idea due to a lot of variation but I have to do it). >In general, you need to run a CDF file through the makecdfenv package >(using either make.cdf.env() or make.cdf.package()) before it can be >used. Then if you want to use that cdvenv with your celfiles, you would >have to read the celfiles into an AffyBatch and then change the cdfName >slot of the AffyBatch to point to your modified cdfenv. > >dat <- ReadAffy() >dat at cdfName <- "nameofyourcdfenv" > >Then proceed as usual. I will do this thank you. Will this work on R 2.1.1 on Windows or do i need to do it on Linux? Also what is the minimum requirement for the structure of the CDF file? Thank you Ruppert. >HTH, > >Jim > > > >Ruppert Valentino wrote: > > >Hello, > > I have created a custom made CDF file and am trying to install >that > >to analyse Affymetrix chip files. Can anyone tell me what format should >the > >CDF files be in? and when does the CEL file has a CDF file attached to >it, > >if so how can I update the CEL file data with my custom made CDF? > > > >Many thanks > > > >Raphael. > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor at stat.math.ethz.ch > >https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > >