Thanks Sam.  Your workaround did the trick.

Fong

On Thu, Sep 9, 2010 at 12:37 AM, Samuel Wuest <wuests@tcd.ie> wrote:

> Hello Fong,
>
> as mentioned earlier, I am reporting the small bug in approxfun, and
> that should get around the pa.calls problem in future releases.
> However, I found that as a quick fix, you can simply round your
> expression-set values to 4 or 5 digits, and then, the problem
> shouldn't occur anymore.
>
> At least, that's what worked for me:
>
> example code:
>
> ...
> eset <- rma(raw.data)
> exprs(eset) <- round(exprs(eset), digits=5)  ### or if that does not
> help, try digits=4
> myCalls <- pa.calls(eset)
>
> or similar.
>
> Best, Sam
>
> On 27 August 2010 18:49, Samuel Wuest <wuests@tcd.ie> wrote:
> > Hi Fong,
> >
> > I have pinpointed the problem to the approxfun-function in the stats
> > package (so the base-contribution of the R-software). So I have posted
> > the exact problem onto R-help mailing list and got back some possible
> > explanation: seems to be a small issue with rounding numbers in
> > approxfun-function in the stats-package (that is called within the
> > pa.calls-function)
> > This has nothing to do with the panp-package but might be a small bug
> > in a base-level function:
> > See also:
> >
> http://r.789695.n4.nabble.com/approxfun-problems-yleft-and-yright-ignored-td2338313.html#a2338313
> >
> > I'll double check and file a bug report, so it should be fixed in
> > coming R-releases.
> >
> > That said, the bug only seems to show up when a particular data
> > structure is present (where you have two very very similar numbers in
> > negative probeset signals and expression set); I have tried out some
> > commonly used data and there, everything went fine.
> >
> > So the pa.calls function should work fine by default and you would
> > only very rarely run into the problem.
> >
> > I'll keep you posted...
> >
> > Best, Sam
> >
> > On 25 August 2010 22:08, Fong Chun Chan <fongchun@interchange.ubc.ca>
> wrote:
> >> Hi Sam,
> >>
> >> Did you ever figure out how to get around this issue?  I am having the
> exact
> >> same issue when I am running pa.calls on my Expression set.  I am also
> running R
> >> version 2.11.1 myself.
> >>
> >> Fong
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >>
> >
> >
> >
> > --
> > -----------------------------------------------------
> > Samuel Wuest
> > Smurfit Institute of Genetics
> > Trinity College Dublin
> > Dublin 2, Ireland
> > Phone: +353-1-896 2444
> > Web: http://www.tcd.ie/Genetics/wellmer-2/index.html
> > Email: wuests@tcd.ie
> > ------------------------------------------------------
> >
>
>
>
> --
> -----------------------------------------------------
> Samuel Wuest
> Smurfit Institute of Genetics
> Trinity College Dublin
> Dublin 2, Ireland
> Phone: +353-1-896 2444
> Web: http://www.tcd.ie/Genetics/wellmer-2/index.html
> Email: wuests@tcd.ie
> ------------------------------------------------------
>

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