Affymetrix reannotation
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Samuel Wuest ▴ 30
@samuel-wuest-2477
Last seen 7.1 years ago
Hi, I trying to assess a modified version of the Affymetrix present/absent call algorithm on my data, which have been generated from two-round amplified RNA hybridized to the Arabidopsis ATH1 GeneChip. I would need some negative control probesets, and thought of probesets that were designed based on wrong gene annotations (similar to what was used in the PANP method from Peter Warren et al.). Therefore, I wondered whether someone does a reannotation of Affy probesets on a regular base? (for example, the version 7 of the Arabidopsis Genome Annotation has been released recently, and some probesets on the AffyChip are most probably not matching any gene model anymore). If yes, where could I find the updated datafiles? Is there anything in the BioC annotation package for the ATH1Chip? Thanks for any help. Best, Sam ----------------------------------------------------- Dipl. Bot. Samuel Wust Dep. of Developmental Genetics Institute for Plant Biology University of Zuerich Zollikerstrasse 107 CH - 8008 Z?rich Phone: +41-(0)44 634 82 42 Mobile: + 41 (0)76 501 69 22 Email: swuest at botinst.uzh.ch
Annotation panp Annotation panp • 854 views
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 5.2 years ago
United States
Samuel Wuest wrote: > Hi, > > I trying to assess a modified version of the Affymetrix present/absent call > algorithm on my data, which have been generated from two-round amplified RNA > hybridized to the Arabidopsis ATH1 GeneChip. > > I would need some negative control probesets, and thought of probesets that > were designed based on wrong gene annotations (similar to what was used in > the PANP method from Peter Warren et al.). > Therefore, I wondered whether someone does a reannotation of Affy probesets > on a regular base? (for example, the version 7 of the Arabidopsis Genome > Annotation has been released recently, and some probesets on the AffyChip > are most probably not matching any gene model anymore). > > If yes, where could I find the updated datafiles? Is there anything in the > BioC annotation package for the ATH1Chip? > > Thanks for any help. > Best, Sam > > ----------------------------------------------------- > Dipl. Bot. Samuel Wust > Dep. of Developmental Genetics > Institute for Plant Biology > University of Zuerich > Zollikerstrasse 107 > CH - 8008 Z?rich > Phone: +41-(0)44 634 82 42 > Mobile: + 41 (0)76 501 69 22 > Email: swuest at botinst.uzh.ch > > _______________________________________________ > 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 > > We provide a "standard" annotation package for this chip. You can find it here: http://bioconductor.org/packages/2.1/data/annotation/html/ath1121501.d b.html Marc
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Thanks a lot, I am familiar with the ath1121501 package. Now I don?t know whether it contains informations on the probe-level rather than on the probeset- level (e.g. whether a designed probe still targets an updated gene model? or which probe-sets are obsolete and can be considered to be outdated?) And: How can I retrieve such information without writing a blast- script to check every single probe against the most updated cDNA database? Thanks for any help on this. Samuel On Tue, 06 Nov 2007 10:31:38 -0800 Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > Samuel Wuest wrote: >> Hi, >> >> I trying to assess a modified version of the Affymetrix present/absent >>call >> algorithm on my data, which have been generated from two-round amplified >>RNA >> hybridized to the Arabidopsis ATH1 GeneChip. >> >> I would need some negative control probesets, and thought of probesets >>that >> were designed based on wrong gene annotations (similar to what was used in >> the PANP method from Peter Warren et al.). >> Therefore, I wondered whether someone does a reannotation of Affy >>probesets >> on a regular base? (for example, the version 7 of the Arabidopsis Genome >> Annotation has been released recently, and some probesets on the AffyChip >> are most probably not matching any gene model anymore). >> >> If yes, where could I find the updated datafiles? Is there anything in the >> BioC annotation package for the ATH1Chip? >> >> Thanks for any help. >> Best, Sam >> >> ----------------------------------------------------- >> Dipl. Bot. Samuel Wust >> Dep. of Developmental Genetics >> Institute for Plant Biology >> University of Zuerich >> Zollikerstrasse 107 >> CH - 8008 Z?rich >> Phone: +41-(0)44 634 82 42 >> Mobile: + 41 (0)76 501 69 22 >> Email: swuest at botinst.uzh.ch >> >> _______________________________________________ >> 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 >> >> > > We provide a "standard" annotation package for this chip. You can find > it here: > > http://bioconductor.org/packages/2.1/data/annotation/html/ath1121501 .db.html > > > Marc >
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Hi Samuel, If you just want to ensure the probes in each probeset actually map to the current genome build, then you might consider the MBNI re-mapped cdfs. For the ath1121501 chip there are two you could consider; the ath1atrefseqcdf or ath1attaircdf packages. The probes were first blasted against this version of the genome (1con.01222004, file date is 08/10/2006) -- not sure what that means, as I am not a plant guy. The probes that mapped to a single unique sequence on the genome were then annotated to genes using either TAIR or RefSeq (this is part of the package name above), so you are assured that any probes that are outdated have been removed. More info is available here (note these are version 10): http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF _download.asp#v10 You can get the package(s) in one of two ways. First, you can get them automagically by doing something like: dat <- ReadAffy(filenames=list.celfiles(), cdfname="ath1atrefseqcdf") or you can download/install using biocLite() and then specify in your call to ReadAffy() (or justRMA()/justGCRMA() if you are going that route). Best, Jim Samuel Wuest wrote: > Thanks a lot, > > I am familiar with the ath1121501 package. Now I don?t know whether it > contains informations on the probe-level rather than on the probeset-level > (e.g. whether a designed probe still targets an updated gene model? or which > probe-sets are obsolete and can be considered to be outdated?) > > And: How can I retrieve such information without writing a blast- script to > check every single probe against the most updated cDNA database? > > Thanks for any help on this. > Samuel > > On Tue, 06 Nov 2007 10:31:38 -0800 > Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > >>Samuel Wuest wrote: >> >>>Hi, >>> >>>I trying to assess a modified version of the Affymetrix present/absent >>>call >>>algorithm on my data, which have been generated from two-round amplified >>>RNA >>>hybridized to the Arabidopsis ATH1 GeneChip. >>> >>>I would need some negative control probesets, and thought of probesets >>>that >>>were designed based on wrong gene annotations (similar to what was used in >>>the PANP method from Peter Warren et al.). >>>Therefore, I wondered whether someone does a reannotation of Affy >>>probesets >>>on a regular base? (for example, the version 7 of the Arabidopsis Genome >>>Annotation has been released recently, and some probesets on the AffyChip >>>are most probably not matching any gene model anymore). >>> >>>If yes, where could I find the updated datafiles? Is there anything in the >>>BioC annotation package for the ATH1Chip? >>> >>>Thanks for any help. >>>Best, Sam >>> >>>----------------------------------------------------- >>>Dipl. Bot. Samuel Wust >>>Dep. of Developmental Genetics >>>Institute for Plant Biology >>>University of Zuerich >>>Zollikerstrasse 107 >>>CH - 8008 Z?rich >>>Phone: +41-(0)44 634 82 42 >>>Mobile: + 41 (0)76 501 69 22 >>>Email: swuest at botinst.uzh.ch >>> >>>_______________________________________________ >>>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 >>> >>> >> >>We provide a "standard" annotation package for this chip. You can find >>it here: >> >>http://bioconductor.org/packages/2.1/data/annotation/html/ath1121501 .db.html >> >> >> Marc >> > > > _______________________________________________ > 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 University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623
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