[BioC] Puzzled with htmlpage

[James W. MacDonald]

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
$ll
[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.


HTH,

Jim
-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623