I am having a little trouble torturing gcrma() into accepting a custom CDF file created locally. (Local in this case is R Ver 2.0.1 on a reasonably recent linux box). I can create and convince R/Bioc to accept a custom CDF file in some cases. It works fine with rma() and mas5() . But ... gcrma uses some "probepackage" thingamajig and goes looking out on the internet for some custom name for the custom cdf library I created and of course does not find it. What function/method do I need to run to create a custom "probe information" file for my custom CDF file how do I make gcrma() use this new information by looking locally for it and not out on the internet? Help. pleez. -rich

Hi, gcrma uses probe sequence information in estimating non-specific binding so you need the probepackge. You can create the probepackge if it's not available on bioconductor. The vignette for 'matchprobes" package has description of the function "makeProbePackage". Here's the link http://bioconductor.org/repository/devel/vignette/././matchprobes.pdf best, Jean On Tue, 8 Mar 2005, Richard Finney wrote: > > I am having a little trouble torturing gcrma() > into accepting a custom CDF file created locally. > (Local in this case is R Ver 2.0.1 on a reasonably > recent linux box). > > I can create and convince R/Bioc to accept > a custom CDF file in some cases. It works > fine with rma() and mas5() . But ... gcrma > uses some "probepackage" thingamajig and goes > looking out on the internet for some custom > name for the custom cdf library I created and > of course does not find it. > > What function/method do I need to run to create > a custom "probe information" file for my custom > CDF file how do I make gcrma() use this new > information by looking locally for it and not > out on the internet? > > Help. pleez. > > -rich > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >