[BioC] pa.calls-function in package "panp"

[Samuel Wuest]

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 at 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
>
> _______________________________________________
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>
>



-- 
-----------------------------------------------------
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 at tcd.ie