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 <
elizabethmcclel...@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
> elizabethmcclel...@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
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