[BioC] a problem with Metadat package: hgu133a2
John Zhang
jzhang at jimmy.harvard.edu
Wed Oct 5 15:02:57 CEST 2005
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
>> >
>>
>
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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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