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 ------------------------------------------------------ [[alternative HTML version deleted]]