Ooops, i wanted to send this to the list, sorry. G.

On Tue, Apr 1, 2008 at 11:03 AM, Gábor Csárdi <csardi.gabor@gmail.com>
wrote:

> Robert, just in case you haven't done it yet. I think it is in
> hyperGTeest-methods.R and after
>
>     ## Num white drawn (n11)
>     numWdrawn <- sapply(curCat2Entrez,
>                         function(x) sum(selected %in% x))
>
> you need to add something like
>
>     if (length(numWdrawn)==0) {
>       numWdrawn <- numeric()
>       names(numWdrawn) <- character()
>     }
>
> or of course there are many equivalent solutions... if i remember well the
> problem is that sapply returns a list() when operating on an empty list.
> Which might be an R bug, actually, unless it is on purpose.
>
> Best,
> Gabor
>
> On Mon, Mar 31, 2008 at 9:45 PM, Robert Gentleman <rgentlem@fhcrc.org>
> wrote:
>
> > Hi Paul,
> >   Thanks for the bug report, it seems that there is an issue when all
> > values are zero, which shows up intermittently.  You can solve it by
> > using try or tryCatch around the call to hyperGTest.  You can simply use
> > a p-value of 1, which is what it will be.
> >
> > You should not be loading the GO package for this (KEGG if anything, and
> > even then, please use KEGG.db, not KEGG).
> >
> [...]
>
>

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