[R] approxfun-problems (yleft and yright ignored)

[Greg Snow]

The plots did not come through, see the posting guide for which attachments are allowed.  It will be easier for us to help if you can send reproducible code (we can copy and paste to run, then examine, edit, etc.).  Try finding a subset of your data for which the problem still occurs, then send the data if possible, or similar simulated data if you cannot send original data.

-- 
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.snow at imail.org
801.408.8111


> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of Samuel Wuest
> Sent: Wednesday, August 25, 2010 8:20 AM
> To: r-help at r-project.org
> Subject: [R] approxfun-problems (yleft and yright ignored)
> 
> 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: wuests at tcd.ie
> ------------------------------------------------------