[BioC] Puzzled with htmlpage

James W. MacDonald jmacdon at med.umich.edu
Fri Apr 8 19:18:28 CEST 2005

Fatima Nunez wrote:
> Dear all,
> There is something that is puzzling me. I am trying to create an html page
> with some results I have. These are the 42 LocusID entries:
Hi Fatima,

The problem here is you are passing a list with 42 LocusIDs, rather than 
a list containing a character vector of those locus ids.

 From the help page:

genelist: A list of character vectors containing ids to be made into
           hypertext links. See details for more information.

So mylistLI should look like this:

 > mylistLI
[1] 10457 440465 2633 4638 etc

You could convert mylistLI to what you need by

mylistLI <- list(ll = unlist(mylistLI))

In addition, you should pass a repository list, because without doing so 
you are relying on the default being correct.

 >htmlpage(mylistLI, filename = "mylist.html", title = "mylist", 
table.center = TRUE, repository=list("ll"))

Also note that LocusLink has been deprecated, so you might want to use

 >htmlpage(mylistLI, filename = "mylist.html", title = "mylist", 
table.center = TRUE, repository=list("en"))

Which will build links to EntrezGene. For this you will need the devel 
version of annotate.


James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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