[R] Help on qpcR package

[Endy BlackEndy]

I am using R on a Windows XP professional platform.
  The following code is part of a bigger one
         CODE
  press=function(y,x){
   library(qpcR)
   models.press=numeric(0)
   cat("\n")
   dep=y
  print(dep)
   indep=log(x)
  print(indep)
   yfit=dep-PRESS(lm(dep~indep))[[2]]
  cat("\n yfit\n")
  print(yfit)
   yfit.orig=yfit
   presid=y-yfit.orig
   press=sum(presid^2)
   cat("\n")
   cat("PRESS =",press,"\n")
  }
  On the command R window I define

- Ignored:

    > x=c(12,24,13,11,23,10,9,17,11,14,18)
    > y=c(10,11,9,8,5,12,11,21,12,13,14)

  then I load the press source code, I run it using the x and y values
  defined before
  and I get the following

    > press(x,y)
  Loading required package: drc
  Loading required package: alr3
  Loading required package: lattice
  Loading required package: magic
  Loading required package: abind
  Loading required package: MASS
  Loading required package: nlme
  Loading required package: plotrix

  'drc' has been loaded.

  Please cite R and 'drc' if used for a publication,
  for references type 'citation()' and 'citation('drc')'.

  Loading required package: gtools
  Loading required package: gplots
  Loading required package: gdata
  Loading required package: caTools
  Loading required package: bitops
  Loading required package: grid

  Attaching package: 'gplots'


          The following object(s) are masked from package:plotrix :

           plotCI


          The following object(s) are masked from package:stats :

           lowess


  'qpcR' has been loaded.

  Please cite R and the following if used for a publication:

  Spiess AN, Feig C, Ritz
  Highly accurate sigmoidal fitting of real-time PCR data by introducing
  a parameter for asymmetry.
  BMC Bioinformatics 2008, 29:221
  or
  Ritz C, Spiess AN. qpcR: an R package for sigmoidal model selection in
  quantitative real-time polymerase chain reaction analysis.
  Bioinformatics 2008, 24:1549-1551

  Newest version always available at www.dr-spiess.de/qpcR.html.


  Attaching package: 'qpcR'


          The following object(s) are masked from package:gplots :

           residplot


   [1] 12 24 13 11 23 10  9 17 11 14 18
   [1] 2.302585 2.397895 2.197225 2.079442 1.609438 2.484907 2.397895
  3.044522 2.484907 2.564949 2.639057
  Error in get(noquote(a)) : object 'dep' not found

  The error reported, as I understand it, is that the object dep it is
  not defined. Obviously, at least to me, it is defined.

  If I declare the dep and indep objects on the command R window i. e.

  > dep=y
  > indep=x

  and rerun the programme  then it runs correctly and gives

  > press(x,y)

   [1] 12 24 13 11 23 10  9 17 11 14 18
   [1] 2.302585 2.397895 2.197225 2.079442 1.609438 2.484907 2.397895
  3.044522 2.484907 2.564949 2.639057

   yfit
   [1] 13.764062 24.199292 15.804140 15.192045 32.465326  9.547579
  9.845243  6.176015 10.521896 12.325493 14.931854

  PRESS = 248.7043

    Can anybody point out what's the problem?
  Thanks in advance
  K. Karakostas