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
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