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Endy BlackEndy

2009-Jun-21 18:02 UTC

[R] Help on qpcR package

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

Ben Bolker

2009-Jun-21 20:54 UTC

head link

[R] Help on qpcR package

Endy BlackEndy wrote:> 
> 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
> 
> 
 You really need to contact the package maintainers about this one.
Since your example is (a) not reproducible by us and (b) involves
a niche package (one for a very specific type of analysis), you're
probably not going to get much help here.  My guess is that the
package is trying to do something clever with environments that
makes their function not work when it is called from inside another
function.  You could try running your function code by hand (i.e.
not from within a function) and see if that makes a difference.

  Ben Bolker

-- 
View this message in context:
http://www.nabble.com/Help-on-qpcR-package-tp24137125p24138733.html
Sent from the R help mailing list archive at Nabble.com.

Ben Bolker

2009-Jun-21 20:55 UTC

head link

[R] Help on qpcR package

Endy BlackEndy wrote:> 
> 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
> 
> 
 You really need to contact the package maintainers about this one.
Since your example is (a) not reproducible by us and (b) involves
a niche package (one for a very specific type of analysis), you're
probably not going to get much help here.  My guess is that the
package is trying to do something clever with environments that
makes their function not work when it is called from inside another
function.  You could try running your function code by hand (i.e.
not from within a function) and see if that makes a difference.

  Ben Bolker

-- 
View this message in context:
http://www.nabble.com/Help-on-qpcR-package-tp24137125p24138743.html
Sent from the R help mailing list archive at Nabble.com.

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