Dear All, I'm trying to use gcrma to analysis the data I have. Unfortunately, I only have cel file and the bpmap file for the arrays. It seems that cdf file is manditory for gcrma, any possibile way I could bypassing it with the bpmap file? Any help will be certainly appreciated. Best, Baoqiang Cao

It depends on what you mean with gcrma. I assume you are using a tiling array since you have bpmap files. On a tiling array there are not really any probesets, which is required by parts of gcrma. What you might be interested in is running the background correction as well as the normalization. And that should be possible witha bit of hand-tweaking I _think_. Kasper On Jan 10, 2007, at 8:39 AM, Baoqiang Cao wrote: > Dear All, > > I'm trying to use gcrma to analysis the data I have. Unfortunately, > I only have cel file and the bpmap file for the arrays. It seems > that cdf file is manditory for gcrma, any possibile way I could > bypassing it with the bpmap file? Any help will be certainly > appreciated. > > Best, > Baoqiang Cao > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor

Hi Baoqiang, have you looked for the cdf-file of your chiptype in the Metadata section of the Bioconductor website? Cheers, Julia Baoqiang Cao wrote: > Dear All, > > I'm trying to use gcrma to analysis the data I have. Unfortunately, I only have cel file and the bpmap file for the arrays. It seems that cdf file is manditory for gcrma, any possibile way I could bypassing it with the bpmap file? Any help will be certainly appreciated. > > Best, > Baoqiang Cao > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >

Hi Julia, I went through the metadata website and couldn't find it. Here is what I got after gcrma: > tmp<-ReadAffy("sample.cel") > gcrma(tmp) Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain Chrom21-22A_2um Library - package chrom2122a2umcdf not installed Data for package affy did not contain chrom2122a2umcdf Bioconductor - chrom2122a2umcdf not available I couldn't find the "chrom2122a2umcdf". Any help will be highly appreciated! Best, Baoqiang ---- Original message ---- >Date: Thu, 11 Jan 2007 10:54:56 +0100 >From: Julia Engelmann <julia.engelmann at="" biozentrum.uni-="" wuerzburg.de=""> >Subject: Re: [BioC] gcrma with bpmap file instead of cdf file >To: caobg at email.uc.edu, bioconductor at stat.math.ethz.ch > >Hi Baoqiang, > >have you looked for the cdf-file of your chiptype in the Metadata >section of the Bioconductor website? > >Cheers, >Julia > > >Baoqiang Cao wrote: >> Dear All, >> >> I'm trying to use gcrma to analysis the data I have. Unfortunately, I only have cel file and the bpmap file for the arrays. It seems that cdf file is manditory for gcrma, any possibile way I could bypassing it with the bpmap file? Any help will be certainly appreciated. >> >> Best, >> Baoqiang Cao >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >

Hi Kasper, Thanks a lot for your reply! Yes, I am using gcrma to run a background correction for tiling array data. "And that should be possible witha bit of hand-tweaking I _think_." Would you please show me any instruction on that then? Thanks again! Best, Baoqiang ---- Original message ---- >Date: Thu, 11 Jan 2007 08:42:25 -0800 >From: Kasper Daniel Hansen <khansen at="" stat.berkeley.edu=""> >Subject: Re: [BioC] gcrma with bpmap file instead of cdf file >To: caobg at email.uc.edu >Cc: bioconductor at stat.math.ethz.ch > >It depends on what you mean with gcrma. I assume you are using a >tiling array since you have bpmap files. On a tiling array there are >not really any probesets, which is required by parts of gcrma. > >What you might be interested in is running the background correction >as well as the normalization. And that should be possible witha bit >of hand-tweaking I _think_. > >Kasper > >On Jan 10, 2007, at 8:39 AM, Baoqiang Cao wrote: > >> Dear All, >> >> I'm trying to use gcrma to analysis the data I have. Unfortunately, >> I only have cel file and the bpmap file for the arrays. It seems >> that cdf file is manditory for gcrma, any possibile way I could >> bypassing it with the bpmap file? Any help will be certainly >> appreciated. >> >> Best, >> Baoqiang Cao >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/ >> gmane.science.biology.informatics.conductor >