CDF/Probe/Annotation for GNF1m custom chip

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Cei Abreu-Goodger ▴ 830

@cei-abreu-goodger-4433

Last seen 9.7 years ago

Mexico

Hello all, I am trying to use affylmGUI to pre-process data from a GNF1m custom Affy chip. I'm on MacOSX 10.4.9, R 2.4.1, Bioconductor 1.9. I downloaded the series CEL file from GEO, and I used make.cdf.package to produce a CDF environment for this chip. I get a warning, but I can install the package anyway, so maybe it's working? Warning message: incomplete final line found by readLines on '/Library/Frameworks/R.framework/Versions/2.4/Resources/library/makecd fenv/Code/DESCRIPTION' But when I try to normalize my CEL files, I get an error stating that the variable "gngnf1musaprobe" was not found. I imagine that, just as I created a custom CDF environment, I now need custom probe and maybe annotation objects. Yet I couldn't find something to indicate how to create these. The affylmGUI help says to ask this mailing list. Does anyone have any suggestions? Thanks, Cei

cdf probe affylmGUI cdf probe affylmGUI • 1.3k views

ADD COMMENT • link updated 17.7 years ago by Kasper Daniel Hansen ★ 6.5k • written 17.7 years ago by Cei Abreu-Goodger ▴ 830

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Kasper Daniel Hansen ★ 6.5k

@kasper-daniel-hansen-2979

Last seen 17 months ago

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On Apr 6, 2007, at 2:02 PM, Cei Abreu-Goodger wrote: > > Hello all, > > I am trying to use affylmGUI to pre-process data from a GNF1m > custom Affy > chip. I'm on MacOSX 10.4.9, R 2.4.1, Bioconductor 1.9. > > I downloaded the series CEL file from GEO, and I used > make.cdf.package to produce a CDF environment for this chip. I get a > warning, but I can install the package anyway, so maybe it's working? > Warning message: > incomplete final line found by readLines on > '/Library/Frameworks/R.framework/Versions/2.4/Resources/library/ > makecdfenv/Code/DESCRIPTION' > > But when I try to normalize my CEL files, I get an error stating > that the > variable "gngnf1musaprobe" was not found. I imagine that, just as I > created a custom CDF environment, I now need custom probe and maybe > annotation objects. Yet I couldn't find something to indicate how to > create these. > The affylmGUI help says to ask this mailing list. Does anyone have any > suggestions? I guess you want to use gcrma. Yes, in that case you need a probe package, which you can create using the matchprobes package. Essentially you will need a file describing the sequence of the probes spotted on the array. The probe package is (essentially, there is some other optional information) a table like x y sequence 1 1 AGCT... This information is certainly not always available, especially since it is not your chip. Sometimes you need a FASTA file, sometimes you can find it in the CDF file or somewhere else. You only need a probe package if you are using a preprocessing procedure that takes the sequence composition of the probes into account - like gcrma. You will not need an annotation package before you want to start to make sense of what "genes" are DE. And you might not need an annotation package for that, depending on what kind of interpretation you want to do. You might need to do some GO annotation in order to do a GO enrichment analysis. Kasper > Thanks, > > Cei > > _______________________________________________ > 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

ADD COMMENT • link 17.7 years ago Kasper Daniel Hansen ★ 6.5k

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Thanks for the reply Kasper. I now have cdf and probe packages for Mouse and Human GNF affy chips. Is there some way I could contribute these to bioconductor? Cei On Fri, 6 Apr 2007, Kasper Daniel Hansen wrote: > > On Apr 6, 2007, at 2:02 PM, Cei Abreu-Goodger wrote: > > > > > Hello all, > > > > I am trying to use affylmGUI to pre-process data from a GNF1m > > custom Affy > > chip. I'm on MacOSX 10.4.9, R 2.4.1, Bioconductor 1.9. > > > > I downloaded the series CEL file from GEO, and I used > > make.cdf.package to produce a CDF environment for this chip. I get a > > warning, but I can install the package anyway, so maybe it's working? > > Warning message: > > incomplete final line found by readLines on > > '/Library/Frameworks/R.framework/Versions/2.4/Resources/library/ > > makecdfenv/Code/DESCRIPTION' > > > > But when I try to normalize my CEL files, I get an error stating > > that the > > variable "gngnf1musaprobe" was not found. I imagine that, just as I > > created a custom CDF environment, I now need custom probe and maybe > > annotation objects. Yet I couldn't find something to indicate how to > > create these. > > The affylmGUI help says to ask this mailing list. Does anyone have any > > suggestions? > > I guess you want to use gcrma. Yes, in that case you need a probe > package, which you can create using the matchprobes package. > Essentially you will need a file describing the sequence of the > probes spotted on the array. The probe package is (essentially, there > is some other optional information) a table like > x y sequence > 1 1 AGCT... > This information is certainly not always available, especially since > it is not your chip. Sometimes you need a FASTA file, sometimes you > can find it in the CDF file or somewhere else. > > You only need a probe package if you are using a preprocessing > procedure that takes the sequence composition of the probes into > account - like gcrma. > > You will not need an annotation package before you want to start to > make sense of what "genes" are DE. And you might not need an > annotation package for that, depending on what kind of interpretation > you want to do. You might need to do some GO annotation in order to > do a GO enrichment analysis. > > Kasper > > > Thanks, > > > > Cei > > > > _______________________________________________ > > 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 > >

ADD REPLY • link 17.7 years ago Cei Abreu-Goodger ▴ 830

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Hi Cei, Cei Abreu-Goodger wrote: > Thanks for the reply Kasper. > > I now have cdf and probe packages for Mouse and Human GNF affy chips. Is > there some way I could contribute these to bioconductor? We only provide cdf and probe packages for commercially available Affy chips, specifically excluding custom chips. There are two reasons for this: 1.) A custom chip implies that the chip was produced specifically for one (or a very small group of) researcher(s). Because these chips won't be widely distributed, it doesn't make sense to spend the time and effort to maintain these packages. 2.) The cdf and probe packages for custom chips are not freely downloadable from Affy's website. We re-build the cdf and probe packages for every release, so we have to be able to easily get the original source data. In addition, there may be legal issues concerning the ownership of the custom chip cdf and probe data that we don't want to get involved with. But thanks for the offer! Best, Jim > > Cei > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

ADD REPLY • link 17.7 years ago James W. MacDonald 67k

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On Apr 9, 2007, at 6:28 AM, James W. MacDonald wrote: > Hi Cei, > > Cei Abreu-Goodger wrote: >> Thanks for the reply Kasper. >> >> I now have cdf and probe packages for Mouse and Human GNF affy >> chips. Is >> there some way I could contribute these to bioconductor? > > We only provide cdf and probe packages for commercially available Affy > chips, specifically excluding custom chips. There are two reasons > for this: > > 1.) A custom chip implies that the chip was produced specifically for > one (or a very small group of) researcher(s). Because these chips > won't > be widely distributed, it doesn't make sense to spend the time and > effort to maintain these packages. > > 2.) The cdf and probe packages for custom chips are not freely > downloadable from Affy's website. We re-build the cdf and probe > packages > for every release, so we have to be able to easily get the original > source data. In addition, there may be legal issues concerning the > ownership of the custom chip cdf and probe data that we don't want to > get involved with. > > But thanks for the offer! Is this also the case where someone offers to maintain the CDF package and the CDF package in question may have a large )at least larger than a single lab) audience (collaborating labs using the same chip). I think I will be in that situation "soon". Kasper > Best, > > Jim > > >> >> Cei >> > > > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and > should not be used for urgent or sensitive issues. > > _______________________________________________ > 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

ADD REPLY • link 17.7 years ago Kasper Daniel Hansen ★ 6.5k

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Kasper Daniel Hansen wrote: > Is this also the case where someone offers to maintain the CDF package > and the CDF package in question may have a large )at least larger than > a single lab) audience (collaborating labs using the same chip). I > think I will be in that situation "soon". We had a discussion about this a couple of years ago and at that time the consensus was that we would only offer those packages that are freely downloadable from Affy. I would still argue for keeping this paradigm, mainly because Affy as a company is particularly worried about the ownership of intellectual property (have you ever read their Terms of Use document that comes with the chips? I'm no lawyer, but it appears to me that you _barely_ have the right to even use the chip, and that point is debatable.). Legal issues aside, a custom chip by definition has an extremely limited group of users, but the amount of work required to host the chip is the same as for something like an hgu133plus2. At some point you have to say that the effort expended to do something is greater than the aggregate benefit for end users, and with limited resources keeping the cost/benefit ratio small is very important. Best, Jim > > Kasper > > >> Best, >> >> Jim >> >> >>> >>> Cei >>> >> >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Affymetrix and cDNA Microarray Core >> University of Michigan Cancer Center >> 1500 E. Medical Center Drive >> 7410 CCGC >> Ann Arbor MI 48109 >> 734-647-5623 >> >> >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should >> not be used for urgent or sensitive issues. >> >> _______________________________________________ >> 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 > > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

ADD REPLY • link 17.7 years ago James W. MacDonald 67k

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