Hello,

I am not sure this post belongs here, but it concerns the pa.calls-function
in the Bioconductor-package "panp" (and probably the approxfun-function
called by pa.calls()). The package provides an alternative to the
MA5-present/absent call calculations based on negative probesets present on
the Affy HGU133A-platform series.

First the question: does the pa.calls-function in the package panp still
work as initially anticipated? Has anyone used it in R version > 2.9.1 and
run into problems?

I have used the function pa.calls and slightly modified it to work on the
ATH1 Arabidopsis platform based on probes that do not match genomic
information anymore. Running the function in R version 2.8 worked fine,
however, after updating to R2.11.1 I run into problems and the error message

"Error in if (x <= tightCutoff) return("P") else if (x > looseCutoff)
return("A") else return("M") :
  missing value where TRUE/FALSE needed" turned up;

The pa.calls-function depends on interpolating expression values from
negative probesets onto expression values from the whole array. The latter
would in some cases lie outside the range of signals derived from the
negative probesets.
I have figured out the the approxfun - function used in pa.calls() has
changed in R 2.9.1:
 "approxfun() and approx() now accept a 'rule' of length two, for easy
specification of different interpolation rules on left and right.", whereby
the default (rule=1) returns NAs if interpolation is to take place outside
the interval [min(x), max(x)];

I think that's where the problem lies... But I might be wrong...

Thanks for any feedback on this issue!

Sam


Here my session info:

> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-apple-darwin9.8.0

locale:
[1] en_IE.UTF-8/en_IE.UTF-8/C/C/en_IE.UTF-8/en_IE.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] panp_1.18.0         ath1121501cdf_2.6.0 tinesath1cdf_1.0.3
affy_1.26.1         Biobase_2.8.0

loaded via a namespace (and not attached):
[1] affyio_1.16.0         preprocessCore_1.10.0 tools_2.11.1

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