Another option is to look at the MLInterfaces package which was partly designed to work with exprSets directly. The function you need is 'knnB'-- you may also want to look at xval for cross-validation.
 
Stephen Henderson

________________________________

From: bioconductor-bounces@stat.math.ethz.ch on behalf of James W. MacDonald
Sent: Sun 02/04/2006 00:54
To: christos@silicoinsights.com
Cc: bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] Classification and the Golub data set



Christos Hatzis wrote:
> I have not used this data, but if golubTest is an expression set,
>
> exprs(golubTest)
>
> will return the expression values as a data frame.  If this does not work,
> try
>
> as.matrix(exprs(golubTest))

Another thing to consider is that most 'classical' statistical methods
expect that the data are in the 'usual' format, with rows as samples and
columns as observations. With microarray data, the opposite convention
holds, with columns as samples and rows as observations. Hence you need
to do:

knn(t(exprs(golubTrain)), t(exprs(golubTest)), cl=golubTrain$ALL.AML, k=3)

Best,

Jim


>
> -Christos
>
> -----Original Message-----
> From: bioconductor-bounces@stat.math.ethz.ch
> [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Chelsea Ellis
> Sent: Saturday, April 01, 2006 3:51 PM
> To: bioconductor@stat.math.ethz.ch
> Subject: [BioC] Classification and the Golub data set
>
> Hi,
>
> I'm just learning Bioconductor, and I'm trying to do KNN classification
> using the Golub test and training sets with ALL and AML as the classifier.
>
> When I use the function
>
> knn(golubTrain, golubTest, cl=golubTrain$ALL.AML, k=3),
>
> it's says that the lengths of the training set and the classifier don't
> match.  The documentation on KNN says you need to have the test and training
> sets in matrix form, but I'm not sure how to change an expression set into a
> matrix.  I tried "unclass" and "as.matrix" with no luck.  This is probably
> an easy question, but I'm stuck.  Thanks for any help you can give.
>
> Chelsea
>
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--
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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