HGU95a and HGU95av2 with gcrma
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@vincent-detours-1021
Last seen 10.2 years ago
Dear all, I need to run gcrma on HGU95a and HGU95av2 arrays. Although the issue came up on the list, no answer was posted. I downloaded hgu95av12mixcdf from http://www.stat.berkeley.edu/~bolstad/mixtureCDF/MixtureCDF.html as recommended in previous postings. RMA ran fine with this later package. In order to run gcrma, I created a hgu95av12mixprobe package with --------- makeProbePackage("hgu95av12mix", datafile = "HG-U95Av2_probe_tab", outdir = ".", maintainer = "Vincent Detours, <vdetours@ulb.ac.be>", version = "0.0.1", force = TRUE) --------- It worked fine. I then installed and loaded all the above data package with "library" and made a combined affybatch with --------- rawc <- combineAffyBatch(list(rawc1, rawc2), c("hgu95av2probe", "hgu95aprobe"), "hgu95av12mix") --------- which ran with no complains. and then ran gcrma: ----------------------- > es <- gcrma(rawc$dat) Computing affinities.Error in compute.affinities(cdfName(object), verbose = verbose) : NAs are not allowed in subscripted assignments > ----------------------- Any idea about what went wrong? An idea would be to make a package from the cdf environment produced by combineAffyBatch. But I don't see how to do this from make.cdf.package, which takes only Affymetrix CDF files as argument. How to make gcrma to use rawc$cdf? Thanks for your help and for all the great work! Vincent Detours, Ph.D. IRIBHM Bldg C, room C.4.116 ULB, Campus Erasme, CP602 808 route de Lennik B-1070 Brussels Belgium Phone: +32-2-555 4220 Fax: +32-2-555 4655 E-mail: vdetours at ulb.ac.be URL: http://homepages.ulb.ac.be/~vdetours/
hgu95a hgu95av2 cdf gcrma hgu95a hgu95av2 cdf gcrma • 2.5k views
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@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
Hi Vincent An idea would be to make a package from the cdf environment produced > by combineAffyBatch. But I don't see how to do this from > make.cdf.package, which takes only Affymetrix CDF files as argument. > How to make gcrma to use rawc$cdf? > What is cdfname(rawc$dat)? Other than creating a new CDF package, I think it should work if you create a variable with that name in your top level workspace that is the CDF environment, e.g. hgu95av12mixcdf = rawc$cdf Let me know if that helps. Bw Wolfgang ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Wellcome Trust Genome Campus Cambridge CB10 1SD England Phone: +44 1223 494642 Phone: +44 1223 4944486 Http: www.ebi.ac.uk/huber
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@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
Question to the gcrma people - how can one make it use a CDF environment that is sitting in the ".GlobalEnv"? (or how to manipulte an environment so that it is recognized?) Best regards Wolfgang -------- Original Message -------- Subject: Re: [BioC] HGU95a and HGU95av2 with gcrma Date: Tue, 23 Nov 2004 11:47:41 +0100 (CET) From: Vincent Detours <vdetours@ulb.ac.be> To: Wolfgang Huber <huber@ebi.ac.uk> > create a variable with that name in your top level workspace that is the > CDF environment, e.g. > > hgu95av12mixcdf = rawc$cdf > > Let me know if that helps. Wolfgang, I tryed it ----------- > cdfName(rawc$dat) [1] "hgu95av12mix" > hgu95av12mixcdf <- rawc$cdf > es <- gcrma(rawc$dat) Computing affinities.Error in compute.affinities(cdfName(object), verbose = verbose) : NAs are not allowed in subscripted assignments > ----------- It doesn't work with gcrma (but it does work with rma). Making a package from rawc$cdf, or forcing getCDF() to use the variable hgu95av12mixcdf would probably work. Any idea of how to do this? Vincent
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Wolfgang Huber wrote: > > Question to the gcrma people - how can one make it use a CDF environment > that is sitting in the ".GlobalEnv"? (or how to manipulte an environment > so that it is recognized?) I would imagine the problem here is with the function getCDF() in compute.affinities(). This is intended to automatically download the correct cdf file if it is not already installed. I didn't include the more sophisticated functionality that Jeff put into getCdfInfo() (which will load the cdf from the .GlobalEnv). However, getCdfInfo() will be called when the affinity.info AffyBatch object is instantiated, so if you simply comment out the line containing getCDF(), I think it should work. HTH, 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
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SInce the cdf environment generated in combineAffyBatch is not a package for a real array, there is no "xy2i" function associated with it, which compute.affinities() uses to link probe sequence and probe location. One options it to compute affinity.info1=compute.affinities("hgu95a") affinity.info2=compute.affinities("hgu95av2") affinity.mix12=combineAffyBatch(list(affinity.info1,affinity.info2), c("hgu95aprobe","hgu95av2probe"), "hgu95av12mix") Then save affinity.mix12 for future use. When calling gcrma, use "affinity.info=affinity.mix12" On Tue, 23 Nov 2004, Wolfgang Huber wrote: > > Question to the gcrma people - how can one make it use a CDF environment > that is sitting in the ".GlobalEnv"? (or how to manipulte an environment > so that it is recognized?) > > > Best regards > Wolfgang > > -------- Original Message -------- > Subject: Re: [BioC] HGU95a and HGU95av2 with gcrma > Date: Tue, 23 Nov 2004 11:47:41 +0100 (CET) > From: Vincent Detours <vdetours@ulb.ac.be> > To: Wolfgang Huber <huber@ebi.ac.uk> > > > create a variable with that name in your top level workspace that is the > > CDF environment, e.g. > > > > hgu95av12mixcdf = rawc$cdf > > > > Let me know if that helps. > > Wolfgang, I tryed it > ----------- > > cdfName(rawc$dat) > [1] "hgu95av12mix" > > hgu95av12mixcdf <- rawc$cdf > > es <- gcrma(rawc$dat) > Computing affinities.Error in compute.affinities(cdfName(object), > verbose = verbose) : > NAs are not allowed in subscripted assignments > > > ----------- > > It doesn't work with gcrma (but it does work with rma). Making a > package from rawc$cdf, or forcing getCDF() to use the variable > hgu95av12mixcdf would probably work. Any idea of how to do this? > > Vincent > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
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