Hello: What is a CDF file and what should be the contents of it (format) and how should I make it. My question is: I have a probe, its coordinates and annotation in tab delim file. Prob X cord <tab> Prob Y cord <tab> type (PM) <tab> pbset name <tab> annotations I have this for u95av2. Now I want to run RMA on on u95av2 chip cel files using my probeset definitions. I removed probes that are not part of sequence and many more. is there a step-wise protocol to make read.celfiles and rma functions understand my definition file. Please help. thank you srini

On Jan 19, 2009, at 12:50 , Srinivas Iyyer wrote: > Hello: > > What is a CDF file and what should be the contents of it (format) > and how should I make it. > > My question is: > I have a probe, its coordinates and annotation in tab delim file. > > > Prob X cord <tab> Prob Y cord <tab> type (PM) <tab> pbset name <tab> > annotations > > I have this for u95av2. > > Now I want to run RMA on on u95av2 chip cel files using my probeset > definitions. I removed probes that are not part of sequence and many > more. > > is there a step-wise protocol to make read.celfiles and rma > functions understand my definition file. If you truly want to create a CDF file, you should browse the archives - this has been discussed a few times recently. You will need to used writeCDF from affxparser. But it seems like what you want is to modify a CDF environment, and do your analysis in Bioconductor. This has also been discussed at length - try searching for something like "how do I remove probes from a CDF environment". Kasper