Dear all, I have run into a problem when running some code implemented in the Bioconductor panp-package (applied to my own expression data), whereby gene expression values of known true negative probesets (x) are interpolated onto present/absent p-values (y) between 0 and 1 using the *approxfun - function*{stats}; when I have used R version 2.8, everything had worked fine, however, after updating to R 2.11.1., I got unexpected output (explained below).
Please correct me here, but as far as I understand, the yleft and yright arguments set the extreme values of the interpolated y-values in case the input x-values (on whose approxfun is applied) fall outside range(x). So if I run approxfun with yleft=1 and yright=0 with y-values between 0 and 1, then I should never get any values higher than 1. However, this is not the case, as this code-example illustrates: > ### define the x-values used to construct the approxfun, basically these are 2000 expression values ranging from ~ 3 to 7: > xNeg <- NegExprs[, 1] > xNeg <- sort(xNeg, decreasing = TRUE) > > ### generate 2000 y-values between 0 and 1: > yNeg <- seq(0, 1, 1/(length(xNeg) - 1)) > ### define yleft and yright as well as the rule to clarify what should happen if input x-values lie outside range(x): > interp <- approxfun(xNeg, yNeg, yleft = 1, yright = 0, rule=2) Warning message: In approxfun(xNeg, yNeg, yleft = 1, yright = 0, rule = 2) : collapsing to unique 'x' values > ### apply the approxfun to expression data that range from ~2.9 to 13.9 and can therefore lie outside range(xNeg): > PV <- sapply(AllExprs[, 1], interp) > range(PV) [1] 0.000 6208.932 > summary(PV) Min. 1st Qu. Median Mean 3rd Qu. Max. 0.000e+00 0.000e+00 2.774e-03 1.299e+00 3.164e-01 6.209e+03 So the resulting output PV object contains data ranging from 0 to 6208, the latter of which lies outside yleft and is not anywhere close to extreme y-values that were used to set up the interp-function. This seems wrong to me, and from what I understand, yleft and yright are simply ignored? I have attached a few histograms that visualize the data distributions of the objects I xNeg, yNeg, AllExprs[,1] (== input x-values) and PV (the output), so that it is easier to make sense of the data structures... Does anyone have an explanation for this or can tell me how to fix the problem? Thanks a million for any help, best, Sam > 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 affy_1.26.1 Biobase_2.8.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 preprocessCore_1.10.0 -- ----------------------------------------------------- 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: wue...@tcd.ie ------------------------------------------------------
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