[BioC] Classification and the Golub data set

Christos Hatzis christos at silicoinsights.com
Sun Apr 2 00:05:04 CEST 2006

I have not used this data, but if golubTest is an expression set,


will return the expression values as a data frame.  If this does not work,



-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Chelsea Ellis
Sent: Saturday, April 01, 2006 3:51 PM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Classification and the Golub data set


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.


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