Thanks, Zhijin, I have, through a backdoor, created the probepackage for a custom CDF. I do have a second question: gcrma() uses the get() function/method. Is there a way to force get() to look locally and not in the "repository" out on the internet? I can't quite figure out the invocation of this bit of magic. [ thanks folks and sorry for the previous mis-communication. i hit the wrong button. ] -rich --- Zhijin Wu <zwu@jhsph.edu> wrote: > 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 > > > >

IT's probably not the problem of "get". Have you installed your probepackage? Where did you install it in? R will try to look online for the packge only when it thinks it's not yet installed. This can happen when 1. it is indeed not installed or 2. it is installed in a directory that R hasn't been told to look into. On Wed, 9 Mar 2005, Richard Finney wrote: > Thanks, Zhijin, I have, through a backdoor, > created the probepackage for a custom CDF. > > I do have a second question: > gcrma() uses the get() function/method. > Is there a way to force get() to look locally > and not in the "repository" out on the internet? > I can't quite figure out the invocation of this > bit of magic. > > [ thanks folks and sorry for the previous > mis-communication. i hit the wrong button. ] > > -rich > > > --- Zhijin Wu <zwu@jhsph.edu> wrote: > > 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 > > > > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >