Drosophila Genome build used for GeneChip Drosophila-2 CDF?
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@david-molnar-3884
Last seen 9.6 years ago
Dear all, I tried to find out in vain from which genome release the current Chip Description File for GeneChip Drosophila-2 was made. Could anybody give me please a hint? Best regards, David Molnar
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@james-w-macdonald-5106
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Hi David, Look at the left margin here: http://www.affymetrix.com/support/technical/datasheets/drosophila2_dat asheet.pdf Best, Jim D?vid Moln?r wrote: > Dear all, > > I tried to find out in vain from which genome release the current Chip > Description File for GeneChip Drosophila-2 was made. > Could anybody give me please a hint? > > Best regards, > David Molnar > > _______________________________________________ > 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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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Hi Jim, thank you for the swift reply. I puzzled over that affymetrix datasheet before, and I should probably have been more specific on that: has affymetrix never updated this CDF based on Drosophila genome release 3.1? Is bioconductor using the unupdated affymetrix CDF? Release 3.1 of the Drosophila genome is from 2003. Data and gene models have considerably improved since then. In the CDF packages on the bioconductor server the date of the files is from 2008. I speculated that somebody might have had a look on them recently. Is this true? Best regards, David 2010/1/12 James W. MacDonald <jmacdon at="" med.umich.edu="">: > Hi David, > > Look at the left margin here: > > http://www.affymetrix.com/support/technical/datasheets/drosophila2_d atasheet.pdf > > Best, > > Jim > > > > D?vid Moln?r wrote: >> >> Dear all, >> >> I tried to find out in vain from which genome release the current Chip >> Description File for GeneChip Drosophila-2 was made. >> Could anybody give me please a hint? >> >> Best regards, >> David Molnar >> >> _______________________________________________ >> 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 > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues >
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Hi David, I guess it depends on what you are really after. The CDF simply maps the locations of the probes on a chip back to their probesets, so there is never any need to update that file (if Affy changed the design of the chip they would just release a new Drosophila chip as they did when they went to the Drosophila 2.0 chip). I sort of assumed you originally meant to ask what genome build the chip was designed against, which is what they show in the pdf I directed you to. Again, this information is set in stone. What may change is what the probes are assumed to bind to. If for instance an EST is later mapped to a particular gene, then the annotation for the probeset directed against the EST may change to reflect the newer annotation. These data are contained in the drosophila2.db package, which in turn is based on the most recent annotation file from Affymetrix. IIRC, Affy updates these annotation files quarterly, so we would have used the newest Affy annotation file as of October 2009 for the release version of this package. Note that annotating the probesets is a non-trivial task, and we are simply taking the probeset -> Entrez Gene ID mappings from Affy and doing the mapping from Entrez Gene to the various other available annotation data. Since the annotation of any genome is a moving target, and it is a long time since 2003, some of the things that the probesets on this chip are intended to interrogate may no longer be interrogated as well (or at all), according to the genome as we now know it. Our annotation packages only take this into account to the extent that the annotation file from Affy does. A different approach to this problem is taken by the folks at MBNI, who create their own CDF files based on the current genome build. If interested, you can see information about these packages at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/gen omic_curated_CDF.asp They have set up a CRAN-style repository that biocLite() knows about, so if interested, you can get their packages directly using biocLite(). Best, Jim D?vid Moln?r wrote: > Hi Jim, > > thank you for the swift reply. I puzzled over that affymetrix > datasheet before, and I should probably have been more specific on > that: has affymetrix never updated this CDF based on Drosophila genome > release 3.1? Is bioconductor using the unupdated affymetrix CDF? > Release 3.1 of the Drosophila genome is from 2003. Data and gene > models have considerably improved since then. In the CDF packages on > the bioconductor server the date of the files is from 2008. I > speculated that somebody might have had a look on them recently. Is > this true? > > Best regards, > David > > > 2010/1/12 James W. MacDonald <jmacdon at="" med.umich.edu="">: >> Hi David, >> >> Look at the left margin here: >> >> http://www.affymetrix.com/support/technical/datasheets/drosophila2_ datasheet.pdf >> >> Best, >> >> Jim >> >> >> >> D?vid Moln?r wrote: >>> Dear all, >>> >>> I tried to find out in vain from which genome release the current Chip >>> Description File for GeneChip Drosophila-2 was made. >>> Could anybody give me please a hint? >>> >>> Best regards, >>> David Molnar >>> >>> _______________________________________________ >>> 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 >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not be >> used for urgent or sensitive issues >> -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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Dear Jim, Marc, list, affymetrix on enquiry: probeset annotations are updated regularly, but the probe to probeset mapping remains unchanged. This means, that they are still based on Drosophila genome build 3.1 and so is bioconductor. I stumbled over customCDFs quite recently, too. Hearing your recommendations and reading through their documentation, they look almost necessary to use. Unfortunately RNAdegradation plots do seem to make difficulties. The problem might be related to the order of probes in the probesets, and which is not entirely clear to me how to circumvent. Anyways thank you for your help so far! David Molnar 2010/1/13 James W. MacDonald <jmacdon at="" med.umich.edu="">: > Hi David, > > I guess it depends on what you are really after. The CDF simply maps the > locations of the probes on a chip back to their probesets, so there is never > any need to update that file (if Affy changed the design of the chip they > would just release a new Drosophila chip as they did when they went to the > Drosophila 2.0 chip). > > I sort of assumed you originally meant to ask what genome build the chip was > designed against, which is what they show in the pdf I directed you to. > Again, this information is set in stone. > > What may change is what the probes are assumed to bind to. If for instance > an EST is later mapped to a particular gene, then the annotation for the > probeset directed against the EST may change to reflect the newer > annotation. These data are contained in the drosophila2.db package, which in > turn is based on the most recent annotation file from Affymetrix. IIRC, Affy > updates these annotation files quarterly, so we would have used the newest > Affy annotation file as of October 2009 for the release version of this > package. > > Note that annotating the probesets is a non-trivial task, and we are simply > taking the probeset -> Entrez Gene ID mappings from Affy and doing the > mapping from Entrez Gene to the various other available annotation data. > Since the annotation of any genome is a moving target, and it is a long time > since 2003, some of the things that the probesets on this chip are intended > to interrogate may no longer be interrogated as well (or at all), according > to the genome as we now know it. Our annotation packages only take this into > account to the extent that the annotation file from Affy does. > > A different approach to this problem is taken by the folks at MBNI, who > create their own CDF files based on the current genome build. If interested, > you can see information about these packages at > > http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/g enomic_curated_CDF.asp > > They have set up a CRAN-style repository that biocLite() knows about, so if > interested, you can get their packages directly using biocLite(). > > Best, > > Jim > > > > D?vid Moln?r wrote: >> >> Hi Jim, >> >> thank you for the swift reply. I puzzled over that affymetrix >> datasheet before, and I should probably have been more specific on >> that: has affymetrix never updated this CDF based on Drosophila genome >> release 3.1? Is bioconductor using the unupdated affymetrix CDF? >> Release 3.1 of the Drosophila genome is from 2003. ?Data and gene >> models have considerably improved since then. In the CDF packages on >> the bioconductor server the date of the files is from 2008. I >> speculated that somebody might have had a look on them recently. Is >> this true? >> >> Best regards, >> David >> >> >> 2010/1/12 James W. MacDonald <jmacdon at="" med.umich.edu="">: >>> >>> Hi David, >>> >>> Look at the left margin here: >>> >>> >>> http://www.affymetrix.com/support/technical/datasheets/drosophila2 _datasheet.pdf >>> >>> Best, >>> >>> Jim >>> >>> >>> >>> D?vid Moln?r wrote: >>>> >>>> Dear all, >>>> >>>> I tried to find out in vain from which genome release the current Chip >>>> Description File for GeneChip Drosophila-2 was made. >>>> Could anybody give me please a hint? >>>> >>>> Best regards, >>>> David Molnar >>>> >>>> _______________________________________________ >>>> 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 >>> Douglas Lab >>> University of Michigan >>> Department of Human Genetics >>> 5912 Buhl >>> 1241 E. Catherine St. >>> Ann Arbor MI 48109-5618 >>> 734-615-7826 >>> ********************************************************** >>> Electronic Mail is not secure, may not be read every day, and should not >>> be >>> used for urgent or sensitive issues >>> > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues >
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Hi David, If your drosophila2 cdf package says it was made in 2008, then you are using an old package (and possibly even an old version of R and Bioconductor). The most recently released package was made in October of 2009. And there will be another new one in the spring. The Bioconductor annotations are updated every 6 months. BUT, if Affymetrix never updates their source materials, then our regular updates will not be any more current for something like a cdf package. While Affy does seem to update a lot of their stuff we don't have the resources to babysit them. We simply get their very latest sources whenever we rebuild these packages. Unless you want to get into the business of remapping probes, we are all ultimately at the mercy of the manufacturers for telling us what they mean and how they map. However, if you feel that the manufacturers claims about their product are inadequate, the MBNI provides MANY alternative mappings for many platforms. They have done a lot of work on this stuff, so if you feel inclined, I would encourage you to explore what they offer. http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF _download.asp Marc D?vid Moln?r wrote: > Hi Jim, > > thank you for the swift reply. I puzzled over that affymetrix > datasheet before, and I should probably have been more specific on > that: has affymetrix never updated this CDF based on Drosophila genome > release 3.1? Is bioconductor using the unupdated affymetrix CDF? > Release 3.1 of the Drosophila genome is from 2003. Data and gene > models have considerably improved since then. In the CDF packages on > the bioconductor server the date of the files is from 2008. I > speculated that somebody might have had a look on them recently. Is > this true? > > Best regards, > David > > > 2010/1/12 James W. MacDonald <jmacdon at="" med.umich.edu="">: > >> Hi David, >> >> Look at the left margin here: >> >> http://www.affymetrix.com/support/technical/datasheets/drosophila2_ datasheet.pdf >> >> Best, >> >> Jim >> >> >> >> D?vid Moln?r wrote: >> >>> Dear all, >>> >>> I tried to find out in vain from which genome release the current Chip >>> Description File for GeneChip Drosophila-2 was made. >>> Could anybody give me please a hint? >>> >>> Best regards, >>> David Molnar >>> >>> _______________________________________________ >>> 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 >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ********************************************************** >> 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 > >
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