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

[Samuel Wuest]

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 at 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 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
> ------------------------------------------------------
>



-- 
-----------------------------------------------------
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