R help - Sep 2008 - issue with varSel.svm.rfe in package MCRestimate

Hello all,

I would like to perform SVM-RFE (Guyon et al. 2002) in R and have only found
one implementation of this algorithm.  The function belongs
to the MCRestimate package but when I try to use it I encounter a problem
- the function appears to be missing a required package or other function
that I simply cannot find available anywhere.

Here is my session info followed by a simple example with the error message
I receive when using the function varSel.svm.rfe:
> sessionInfo()
R version 2.7.1 (2008-06-23)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] tools     splines   stats     graphics  grDevices utils     datasets
[8] methods   base
other attached packages:
[1] MCRestimate_1.4.0   Biobase_2.0.1       randomForest_4.5-25
[4] pamr_1.38.0         survival_2.34-1     cluster_1.11.11
[7] e1071_1.5-18        class_7.2-42       
RColorBrewer_1.0-2
>
> m<-matrix(c(1:16),4,4)
> classes<-c(1,1,0,0)
> varSel.svm.rfe(m,classes)
Loading required package: rfe
Error in varSel.svm.rfe(m, classes) : could not find function "rfe.cv"
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return
= TRUE,  :
  there is no package called 'rfe'

Thanks in advance for any help/suggestions,
Elizabeth McClellan
elizabethmcclellan@gmail.com


-- 
Ms. Elizabeth McClellan
Research Assistant
Department of Statistical Science
Southern Methodist University

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Unfortunately no one ever answered my question and I was never able to
implement the varSel.svm.rfe function in R.  I found a 2005 book that
mentions the RFE package: Analyzing Microarray Gene Expression Data, Chapter
6.13.4<http://books.google.com/books?id=gt8JNQfpnMIC&pg=PA206&lpg=PA206&dq=>
but
the link does not work so I searched the name Ambroise and came up with this
site: Christophe
Ambroise<http://stat.genopole.cnrs.fr/dw/~cambroise/doku.php?id=softwares:softwares>
.
 Towards the bottom of the page you'll find links to packages that are
supposed to carry out RFE - you might try
RMagpie<http://www.maths.uq.edu.au/bioinformatics/rmagpie.html> .
 I have not yet attempted to use this package.

Elizabeth


On Fri, Sep 26, 2008 at 10:38 AM, Elizabeth McClellan <
elizabethmcclellan@gmail.com> wrote:
> Hello all,
>
> I would like to perform SVM-RFE (Guyon et al. 2002) in R and have only
> found one implementation of this algorithm.  The function belongs
> to the MCRestimate package but when I try to use it I encounter a problem
> - the function appears to be missing a required package or other function
> that I simply cannot find available anywhere.
>
> Here is my session info followed by a simple example with the error message
> I receive when using the function varSel.svm.rfe:
>
> > sessionInfo()
> R version 2.7.1 (2008-06-23)
> i386-pc-mingw32
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> attached base packages:
> [1] tools     splines   stats     graphics  grDevices utils     datasets
> [8] methods   base
> other attached packages:
> [1] MCRestimate_1.4.0   Biobase_2.0.1       randomForest_4.5-25
> [4] pamr_1.38.0         survival_2.34-1     cluster_1.11.11
> [7] e1071_1.5-18        class_7.2-42        RColorBrewer_1.0-2
> >
> > m<-matrix(c(1:16),4,4)
> > classes<-c(1,1,0,0)
> > varSel.svm.rfe(m,classes)
> Loading required package: rfe
> Error in varSel.svm.rfe(m, classes) : could not find function
"rfe.cv"
> In addition: Warning message:
> In library(package, lib.loc = lib.loc, character.only = TRUE,
> logical.return = TRUE,  :
>   there is no package called 'rfe'
>
> Thanks in advance for any help/suggestions,
> Elizabeth McClellan
> elizabethmcclellan@gmail.com
>
>
> --
> Ms. Elizabeth McClellan
> Research Assistant
> Department of Statistical Science
> Southern Methodist University
>


-- 
Ms. Elizabeth McClellan
Research Assistant
Department of Statistical Science
Southern Methodist University

	[[alternative HTML version deleted]]