[BioC] amigo links: gene ontology annotation for probes

[Yvonne J.K. Edwards]

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_NAME=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

-- 
----------------------------------------------------------------------
Yvonne JK Edwards, PhD
Senior Research Fellow
Bioinformatics Unit
Department of Computer Science
University College London
Gower Street, London, WC1E 6BT