Question: UPDATE: a problem with Metadat package: hgu133a2 ----- Fwd: RE: Should BE964473 be mapped to Hs. 333958 or Hs. 282260?
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gravatar for Shi, Tao
14.3 years ago by
Shi, Tao720
Shi, Tao720 wrote:
FYI ...Tao --- "Tao, Tao (NIH/NLM/NCBI)" <tao at="" ncbi.nlm.nih.gov=""> wrote: > From: "Tao, Tao (NIH/NLM/NCBI)" <tao at="" ncbi.nlm.nih.gov=""> > To: "'shidaxia at yahoo.com'" <shidaxia at="" yahoo.com=""> > CC: "Tao, Tao (NIH/NLM/NCBI)" <tao at="" ncbi.nlm.nih.gov=""> > Subject: RE: Should BE964473 be mapped to Hs. 333958 or Hs. 282260? > Date: Wed, 12 Oct 2005 11:38:35 -0400 > > Hi, > > Thanks for your forwarded information. > > This EST is of poor quality with many misread as can be seen from the > chromograph: > > http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=retrieve&val=467194 71&file= > trace&dopt=trace > > I do agree that this EST was assigned to a wrong cluster. Based on the poor > quality above, I will forward a report to our developers to see if we can > remove it from the future UniGene construction. > > Tao Tao, Ph.D. > NCBI USEr service > > ------------- Begin Forwarded Message ------------- > > X-SBRS: 5.5 > X-BrightmailFiltered: true > X-Brightmail-Tracker: AAAAAA== > DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; > h=Message-ID:Received:Date:From:Subject:To:MIME-Version:Content- Type:Content > -Tr > ansfer-Encoding; > b=eHJZKzmbdzBBndPQkox4gIuXgH5dWP5bjMe/GuCCgTgYOo4jAW3diDWwkH820SwS0H DMNYuZKZ > 03B > IVmb9eHQL3Yc/v7ozgWsaXx1+kO1xGa0sbLEHAciOKF6knTLDBplOIrvk7Emu0aprCYA qXnMhAiA > abm > xu7R5V8odAfJr4I= ; > Date: Mon, 10 Oct 2005 09:51:13 -0700 (PDT) > From: "Shi, Tao" <shidaxia at="" yahoo.com=""> > Subject: Should BE964473 be mapped to Hs. 333958 or Hs. 282260? Fwd: Re: > > [BioC] a problem with Metadat package: hgu133a2 > To: info at ncbi.nlm.nih.gov > MIME-Version: 1.0 > Content-Transfer-Encoding: 8bit > X-Scanned-By: MIMEDefang 2.36 > > Please see below. Thanks, > > ...Tao > > > > --- Ting-Yuan Liu <tliu at="" fhcrc.org=""> wrote: > > > Date: Mon, 10 Oct 2005 01:22:10 -0700 (PDT) > > From: Ting-Yuan Liu <tliu at="" fhcrc.org=""> > > To: "Shi, Tao" <shidaxia at="" yahoo.com=""> > > CC: bioconductor at stat.math.ethz.ch > > Subject: Re: [BioC] a problem with Metadat package: hgu133a2 > > > > > > Hi Tao, > > > > Please report your observation to NCBI. After NCBI fixes this bug, our > > packages will be updated while we use their new information. > > > > Thanks for this observation. > > > > Best, > > Ting-Yuan > > > > On Wed, 5 Oct 2005, Shi, Tao wrote: > > > > > Hi John, > > > > > > Thank you very much for clearfying it. I see your point. > > > > > > But I really have no idea why NCBI maps BE964473 to Hs. 333958, since > all > the top hits from > > > BLASTing the 221770_at target sequence or BE964473 itself have > annotation > of > > > 'ribulose-5-phosphate-3-epimerase', which should belong to UniGene > cluster > Hs.282260. One > > > interesting thing is that BE964473 and the most of sequences in > Hs.282260 > and some other > > sequences > > > used to belong to a same currently-retired UniGene cluster, Hs.125845. > > > > > > I guess NetAffx won this one........ > > > > > > best, > > > > > > ...Tao > > > > > > > > > --- John Zhang <jzhang at="" jimmy.harvard.edu=""> wrote: > > > > > > > 221770_at is mapped to BE964473 by the chip manufacture and thus to > Hs.333958 > > > > according to UniGene. BioC builds the annotation packages base on NCBI > > and does > > > > not guarantee that the annotation will agree with that from other > sources. It is > > > > totally up to you whether to trust NCBI or NetAffx. > > > > > > > > > > > > > > > > >X-Original-To: jzhang at jimmy.harvard.edu > > > > >Delivered-To: jzhang at jimmy.harvard.edu > > > > >DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; > d=yahoo.com; > > > > > h=Message-ID:Received:Date:From:Subject:To:Cc:In-Reply-To:MIME- Version:Conte > nt- > T > > > > ype:Content-Transfer-Encoding; > > > > > b=MHVPEHM+OGZuRyQIH/S7QAVSX7LpLy9jD3934Q9H/QW8tvzoIyhHrx8EIfLssadFoM 6NHdNtUF > C28 > q > > > > > bRWMWZTjsjWK1XjQrn3wnxR4wlqNuPR3+VfEXujY4Fg36mU/t198aJ0csBkraChJgrxk jWYp2+dB > y/G > Y > > > > 8GK2/Gx8mw3J0= ; > > > > >Date: Tue, 4 Oct 2005 16:39:50 -0700 (PDT) > > > > >From: "Shi, Tao" <shidaxia at="" yahoo.com=""> > > > > >To: Ting-Yuan Liu <tliu at="" fhcrc.org=""> > > > > >MIME-Version: 1.0 > > > > >Received-SPF: pass hypatia.math.ethz.ch: 129.132.145.15 is > authenticated by a > > > > trusted mechanism) > > > > >Received-SPF: none (hypatia: domain of shidaxia at yahoo.com does not > designate > > > > permitted sender hosts) > > > > >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch > > > > >Cc: bioconductor at stat.math.ethz.ch > > > > >Subject: Re: [BioC] a problem with Metadat package: hgu133a2 > > > > >X-BeenThere: bioconductor at stat.math.ethz.ch > > > > >X-Mailman-Version: 2.1.6 > > > > >List-Id: The Bioconductor Project Mailing List > <bioconductor.stat.math.ethz.ch> > > > > >List-Unsubscribe: > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, > > > > <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="unsubscribe"> > > > > >List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor=""> > > > > >List-Post: <mailto:bioconductor at="" stat.math.ethz.ch=""> > > > > >List-Help: > <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="help"> > > > > >List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, > > > > > <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="subscribe"> > > > > >Content-Transfer-Encoding: 7bit > > > > >X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on > > > > pascal.dfci.harvard.edu > > > > >X-Spam-Level: > > > > >X-Spam-Status: No, score=-2.2 required=3.0 tests=AWL,BAYES_00 > autolearn=ham > > > > version=3.0.1 > > > > > > > > > >Hi Ting-Yuan, > > > > > > > > > >Sorry for my forgetfulness. I was thinking about providing the > package > version > > > > information before > > > > >I sent the email out, but still forgot it. > > > > > > > > > >Anyway, here are the information you need: > > > > > > > > > >> sessionInfo() > > > > >R version 2.1.1, 2005-06-20, i386-pc-mingw32 > > > > > > > > > >attached base packages: > > > > >[1] "splines" "tools" "methods" "stats" "graphics" > "grDevices" > > > > "utils" > > > > >[8] "datasets" "base" > > > > > > > > > >other attached packages: > > > > >hgu133plus2 KEGG hgu95av2 GOstats multtest > genefilter > > > > survival > > > > > "1.8.4" "1.8.1" "1.8.4" "1.1.3" "1.6.0" > "1.6.3" > > > > "2.18" > > > > > xtable RBGL annotate graph Biobase > Ruuid > > > > cluster > > > > > "1.2-5" "1.3.13" "1.5.16" "1.5.9" "1.5.12" > "1.5.3" > > > > "1.10.1" > > > > > GO TSP hu6800 hgu133a2 > > > > > "1.8.2" "0.1" "1.8.4" "1.8.4" > > > > > > > > > > > > > > >I got the NetAffx annotation from the NetAffx analysis center where > you > can > > > > input your probe set > > > > >ID and get the annotation interactively. I've also checked the affy > annotation > > > > file > > > > >("HG-U133A_2_annot.csv") I downloaded on 6/20/05 from this website > > > > > >(http://www.affymetrix.com/support/technical/byproduct.affx?product =hgu133- > 20) > . > > > > It has the same > > > > >annotation as shown on the NetAffx website now. I was also > suspecting > that > > > > Affy changed their > > > > >annotations after the package was released, until I checked another > hgu133a2 > > > > annotation file I > > > > >have ("HG-U133A_2 gene info.xls", which I downloaded from dChip > website > on > > > > 2/2004). It's > > > > >annotation is also consistent with the current NetAffx anno. > > > > > > > > > >...Tao > > > > > > > > > > > > > > > > > > > >--- Ting-Yuan Liu <tliu at="" fhcrc.org=""> wrote: > > > > > > > > > >> > > > > >> Hi Tao, > > > > >> > > > > >> ChenWei is not the current maintainer for the meta data packages, > but > I > > > > >> will try to figure what's wrong here for him. > > > > >> > > > > >> Could you provide the result of sessionInfo()? People can get more > > > > > >> information about the versions of the packages you are using and > then > will > > > > >> be easier to determine the source of problem you have. > > > > >> > > > > >> Also, could you tell me which file did you get from NetAffx? When > was > > > > >> this file release? Affymetrix released their annotation files at > least > > > > >> twice after our last release on May. If you are comparing the > package > of > > > > >> BioC 1.6 with the file you recently downloaded, you might find that > > there > > > > >> are some inconsistent because Affymetrix updated the file. > > > > >> > > > > >> Any way, please provide the information I mentioned above so that I > > can > > > > >> determine if you were in such a inconsistent situation. > > > > >> > > > > >> Best, > > > > >> Ting-Yuan > > > > >> > > > > >> On Tue, 4 Oct 2005, Shi, Tao wrote: > > > > >> > > > > >> > Hi Chenwei, > > > > >> > > > > > >> > I ran into this problem totally by random. The annotation for > this > > > > particular probeset is > > > > >> > diffrent from what I got from NetAffx: > > > > >> > > > > > >> > > version > > > > >> > _ > > > > >> > platform i386-pc-mingw32 > > > > >> > arch i386 > > > > >> > os mingw32 > > > > >> > system i386, mingw32 > > > > >> > status > > > > >> > major 2 > > > > >> > minor 1.1 > > > > >> > year 2005 > > > > >> > month 06 > > > > >> > day 20 > > > > >> > language R > > > > >> > > get("221770_at", hgu133a2GENENAME) > > > > >> > [1] "solute carrier family 4, sodium bicarbonate > transporter-like, > member > > > > 10" > > > > >> > > > > > >> > which should be for "206830_at". > > > > >> > > > > > >> > > get("206830_at", hgu133a2GENENAME) > > > > >> > [1] "solute carrier family 4, sodium bicarbonate > transporter-like, > member > > > > 10" > > > > >> > > > > > >> > > > > > >> > The annotation I got from NetAffx is: > > > > >> > > > > > >> > 221770_at ribulose-5-phosphate-3-epimerase > > > > >> > > > > > >> > > > > > >> > Could you please check what's going on? Thanks, > > > > >> > > > > > >> > ...Tao > > > > >> > > > > > >> > _______________________________________________ > > > > >> > Bioconductor mailing list > > > > >> > Bioconductor at stat.math.ethz.ch > > > > >> > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > >> > > > > > >> > > > > > > > > > >_______________________________________________ > > > > >Bioconductor mailing list > > > > >Bioconductor at stat.math.ethz.ch > > > > >https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > > > > Jianhua Zhang > > > > Department of Medical Oncology > > > > Dana-Farber Cancer Institute > > > > 44 Binney Street > > > > Boston, MA 02115-6084 > > > > > > > > > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor at stat.math.ethz.ch > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > > > > > > __________________________________ > Yahoo! Music Unlimited > Access over 1 million songs. Try it free. > http://music.yahoo.com/unlimited/ > > ------------- End Forwarded Message ------------- >
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