[BioC] UPDATE: a problem with Metadat package: hgu133a2 ----- Fwd: RE: Should BE964473 be mapped to Hs. 333958 or Hs. 282260?

Shi, Tao shidaxia at yahoo.com
Thu Oct 13 02:00:35 CEST 2005


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=46719471&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
> 
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> 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
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> 
> 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
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> C28
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> > > > 
> bRWMWZTjsjWK1XjQrn3wnxR4wlqNuPR3+VfEXujY4Fg36mU/t198aJ0csBkraChJgrxkjWYp2+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>
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> > > > >Cc: bioconductor at stat.math.ethz.ch
> > > > >Subject: Re: [BioC] a problem with Metadat package: hgu133a2
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> > > > 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
> > > 
> > 
> 
> 
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