[BioC] How to do k-fold validation using SVM

[Stephen Henderson]

Is there a simple??? way to do a gene/feature selection for each round of
cross validation-- using the ipred errorest function?

I do not mean select some set of genes and then do a cv on this subset, but
rather to reselect the subset for each fold?

I had written a rather long winded loop previous to this posting (had missed
ipred) but now wonder if there is a shortcut?

-----Original Message-----
From: Torsten Hothorn [mailto:Torsten.Hothorn@rzmail.uni-erlangen.de] 
Sent: Friday, January 24, 2003 7:13 AM
To: Adaikalavan Ramasamy
Cc: Song, Guangchun; bioconductor@stat.math.ethz.ch
Subject: RE: [BioC] How to do k-fold validation using SVM

On Fri, 24 Jan 2003, Adaikalavan Ramasamy wrote:

> You might want to use the function svm() in the e1071 library with the
> option 'cross'.
>
> Or you can manually break the dataset into k subsets and write a loop.
> This might be better if you prefer to do stratified sampling for the
> fold rather than random sampling.
>

or you can use the "errorest" function in the ipred-package (see R News
2(2) for examples)

Torsten

> -----Original Message-----
> From: Song, Guangchun [mailto:Guangchun.Song@stjude.org]
> Sent: Friday, January 24, 2003 7:35 AM
> To: bioconductor@stat.math.ethz.ch
> Subject: [BioC] How to do k-fold validation using SVM
>
>
>
> Did anyone know how to do the k-fold validation on the training data set
> by SVM?
>
> Thanks.
>
>
> Guangchun
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
>

_______________________________________________
Bioconductor mailing list
Bioconductor@stat.math.ethz.ch
http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor


**********************************************************************
This email and any files transmitted with it are confidential an ... [[dropped]]