[BioC] Rat 230 2.0 annotation package

[Steffen Durinck]

Hi,

Annotation for this array is available also via the biomaRt package.
The array is known there as rat230_2.  You can use as follows:

 > mart<-martConnect()
 > getGene(id="1387055_at", array="rat230_2",mart=mart)
Slot "id":
[1] "1387055_at"

Slot "table":
$symbol
[1] "APBP1_RAT"

$description
[1] "Amyloid protein-binding protein 1 (Amyloid beta protein- binding 
protein 1, 59 kDa) (APP-BP1). [Source:Uniprot/SWISSPROT;Acc:Q9Z1A5]"

$band
[1] "p14"

$chromosome
[1] "19"

$start
[1] 382556

$end
[1] 408667

$martID
[1] "ENSRNOG00000033133"


 > getGO(id="1387055_at", array="rat230_2",mart=mart)
An object of class "martTable"
Slot "id":
[1] "1387055_at" "1387055_at" "1387055_at" "1387055_at"

Slot "table":
$GOID
[1] "GO:0016874" "GO:0006512" "GO:0006915" "GO:0007049"

$description
[1] "ligase activity" "ubiquitin cycle" "apoptosis"       "cell cycle"

$evidence
[1] "IEA" "IEA" "IEA" "IEA"

$martID
[1] "ENSRNOG00000033133" "ENSRNOG00000033133" "ENSRNOG00000033133"
[4] "ENSRNOG00000033133"


best,
Steffen

David Kipling wrote:

> Hi
>
> Although I can find the rae230a and rae230b rat annotation metadata 
> packages on the Bioconductor site, there doesn't seem to be one for 
> the rat 230 2.0 chip (which is the combination of rae230a and rae230b).
>
> Is one available anywhere, and if not what would be the easiest way to 
> make one (e.g. is is feasible to merge the two existing packages)?
>
> Many thanks
>
> David
>
> Prof David Kipling
> Department of Pathology
> School of Medicine
> Cardiff University
> Heath Park
> Cardiff CF14 4XN
>
> Tel:  029 2074 4847
> Email:  KiplingD at cardiff.ac.uk
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>