[BioC] amigo links: gene ontology annotation for probes

[Colin A. Smith]

Yvonne-

It looks like they changed their URL format. Please look for a fix in  
the next couple days in either annaffy 1.6.2 (Release 1.9) or 1.7.3  
(Devel 2.0).

Cheers.

-Colin

On Feb 19, 2007, at 4:49 , Yvonne J.K. Edwards wrote:

> Hi,
>
> I am using Bioconductor to annotate some probes as described in the
> chapter "Interactive Outputs". CA Smith, W Huber and R. Gentleman, in
> the book "Bioinformatics and Computational Biology Solutions using  
> R and
> Bioconductor". I created the HTML Table with annotation links and
> I noticed that the Gene Ontology link to the Amigo homepage as
> opposed to the GO term in the Amigo site. Judging how interactive the
> other parts of the table are I am suspecting this is not what is  
> intended.
>
> A typical link would look like this
> http://www.godatabase.org/cgi-bin/amigo/go.cgi?open_0=GO:0005554
>
> but the browser displays the home page of amigo.
>
>
> This is sample code
> -------------------
> library("mgu74av2")
> library("XML")
> library("KEGG")
> library("GO")
> library("annotate")
> library("annaffy")
> probeId <- c("103753_at")
> probeId
> anncols <- aaf.handler()[c(1:13)]
> anncols
> annTable <- aafTableAnn(probeId,"mgu74av2", anncols)
> saveHTML(annTable, "annotation.html", title = "Example Table with  
> Data")
>
> This is version of packages
> ---------------------------
> sessionInfo()
> R version 2.4.0 (2006-10-03)
> i686-pc-linux-gnu
> locale:
> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB 
> .UTF-8;LC_
> MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_N 
> AME=C;LC_A
> DDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"      
> "datasets"
> [7] "base"
>
> other attached packages:
> annaffy annotate  Biobase       GO     KEGG      XML mgu74av2
> "1.6.0" "1.12.0" "1.12.2" "1.14.0" "1.14.0"  "1.4-1" "1.14.0"
>
>
> Any suggestions about what I could do to remedy this ??
>
> Thank you for your considerations,
> Best wishes
> Yvonne