[BioC] a problem with Metadat package: hgu133a2
Shi, Tao
shidaxia at yahoo.com
Wed Oct 5 18:56:29 CEST 2005
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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> >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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