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.

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? 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. 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 > > ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

Hi Ruppert, I guess I am still a bit confused. Do you have a custom chip that Affy made for you? If so, they should be able to give you the cdf that comes with that chip. I don't know how else you have a mixture chip, but trying to come up with a cdf by hand would be a daunting task to say the least. The cdf maps the (X,Y) coordinates of each probe back to the probes themselves, so making a mixture cdf presupposes some knowledge of where each probe is located on the chip. I don't know of any way to know this other than by Affy telling you where they put things. Is this what you are trying to do, or are you simply trying to combine data from two different chips somehow? Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "Ruppert Valentino" <ruppert7 at="" hotmail.com=""> 08/22/05 10:57 AM >>> >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 > > > > > _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.