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
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
>
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=hg
u133-20). 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
> >
>
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-
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ype:Content-Transfer-Encoding;
b=MHVPEHM+OGZuRyQIH/S7QAVSX7LpLy9jD3934Q9H/QW8tvzoIyhHrx8EIfLssadFoM6N
HdNtUFC28q
bRWMWZTjsjWK1XjQrn3wnxR4wlqNuPR3+VfEXujY4Fg36mU/t198aJ0csBkraChJgrxkjW
Yp2+dBy/GY
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
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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=h
gu133-20).
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
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:Content-T
> ype:Content-Transfer-Encoding;
> b=MHVPEHM+OGZuRyQIH/S7QAVSX7LpLy9jD3934Q9H/QW8tvzoIyhHrx8EIfLssadFoM
6NHdNtUFC28q
> bRWMWZTjsjWK1XjQrn3wnxR4wlqNuPR3+VfEXujY4Fg36mU/t198aJ0csBkraChJgrxk
jWYp2+dBy/GY
> 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="">,
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> >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
>
>
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:Content-T
> > ype:Content-Transfer-Encoding;
> > b=MHVPEHM+OGZuRyQIH/S7QAVSX7LpLy9jD3934Q9H/QW8tvzoIyhHrx8EIfLssadF
oM6NHdNtUFC28q
> > bRWMWZTjsjWK1XjQrn3wnxR4wlqNuPR3+VfEXujY4Fg36mU/t198aJ0csBkraChJgr
xkjWYp2+dBy/GY
> > 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
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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?produ
ct=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
> >
> >
>
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