[BioC] hgu133plus2SYMBOL missing an entry for 211506_s_at

[sdurinck at ebi.ac.uk]

Hi Dick,

The affy annotation is correct. I'm working on an alternative Bioconductor
package (biomaRt) that can be used for annotation and retrieves the
annotation directly from Ensembl (http://www.ensembl.org). You can find
the biomaRt package in the developmental packages if you want to give it a
try.
This is what it returned for your query:

>library(biomaRt)
> mart<-martConnect()
-  Connected to ensembl_mart_28_1, vega_mart_28_1, snp_mart_28_1 and
sequence_mart_28_1 -
> getGene(id="211506_s_at",array="hgu133plus2",mart=mart)
An object of class "martTable"
Slot "id":
[1] "211506_s_at"

Slot "table":
$symbol
[1] "IL8"

$description
[1] "Interleukin-8 precursor (IL-8) (CXCL8) (Monocyte-derived neutrophil
chemotactic factor) (MDNCF) (T-cell chemotactic factor) (Neutrophil-
activating protein 1) (NAP-1) (Protein 3-10C) (Granulocyte chemotactic
protein 1) (GCP-1) (Monocyte derived neutrophil activating peptide)
(MONAP) (Emoctakin) [Contains: MDNCF-a (IL8/NAP1 form I) (GCP/IL-8 protein
IV); IL-8(1-77) (MDNCF-b) (IL8/NAP1 form II) (GCP/IL-8 protein II)
((ala-IL-8)77); IL-8(6-77) (Lymphocyte-derived neutrophil- activating
factor) (LYNAP) (Neutrophil-activating factor) (NAF) (MDNCF-c) (IL8/NAP1
form III) (GCP/IL-8 protein I) ((ser-IL-8)72); IL- 8(7-77) (IL8/NAP1 form
IV) (GCP/IL-8 protein V); IL-8(8-77) (IL8/NAP1 form V) (GCP/IL-8 protein
VI); IL-8(9-77) (IL8/NAP1 form VI) (GCP/IL-8 protein III)].
[Source:Uniprot/SWISSPROT;Acc:P10145]"

$band
[1] "q13.3"

$chromosome
[1] "4"

$start
[1] 74971310

$end
[1] 74974466

$martID
[1] "ENSG00000169429"


Cheers,
Steffen


I ran into an oddity that I thought others working with hgu133plus2 chips
might want to know.

hgu133plus2SYMBOL is missing an entry for 211506_s_at.

> library(annaffy)
> library(hgu133plus2)
> library(hgu133plus2cdf)
> library(hgu133plus2probe)
> probeids <- ls(hgu133plus2SYMBOL)
> probeids[20834]

[1] "211506_s_at"

> getText(aafSymbol(probeids[20834], "hgu133plus2"))

[1] ""

But the netaffx website shows the Gene Symbol for 211506_s_at as IL8.

Here's my setup:
base 2.0.1 datasets 2.0.1 utils 2.0.1 grDevices 2.0.1 graphics 2.0.1 stats
2.0.1 methods 2.0.1 tools 2.0.1 Biobase 1.5.0 reposTools 1.5.1 affy 1.5.8
GO 1.6.8 KEGG 1.6.8 annotate 1.5.1 annaffy 1.0.11 hgu133plus2 1.6.8 nlme
3.1-53 hgu133plus2cdf 1.4.3 xtable 1.2-4 matchprobes 1.0.12
hgu133plus2probe 1.0

Cheers,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D.    University of Washington
Tel.:(206) 616 7378    Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696    4225 Roosevelt Way NE, # 100
            Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html

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