[BioC] goHyperG generates GO links at arrays.ucsf.edu withwrong perl script,

Paquet, Agnes apaquet at medsfgh.ucsf.edu
Sat Oct 15 00:39:29 CEST 2005

Hi Saurin,

>From the example code you gave, you are generating your html page using the function table2html, which is in the package marray, not GOstats. By default, this function will create a link to annotations provided by the Functional Genomics Core Facility at UCSF for any column name in your data matrix containing "ID". These annotations are provided for Operon and MEEBO oligonucleotides only. This script does not take Gene Ontology identifiers (e.g. GO:xxxxxx) as argument, which explains why you are getting a weird link.

To avoid this problem, you need to set up the correct  URL mapping using the function mapGeneInfo. If you don't want to create any link for your GO ID column, you can use something like:
mymap <- maGeneInfo(ID="none")
table2html(GOtable, file="myFile.html",map=mymap,disp="file")

More details about these functions can be found in the corresponding help files.



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