[BioC] a problem with Metadat package: hgu133a2
Ting-Yuan Liu
tliu at fhcrc.org
Mon Oct 10 10:22:10 CEST 2005
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.
> >
> >
> >
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> > >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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> > >
> > >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
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> >
> > Jianhua Zhang
> > Department of Medical Oncology
> > Dana-Farber Cancer Institute
> > 44 Binney Street
> > Boston, MA 02115-6084
> >
> >
>
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