[BioC] Applying classifiers derived from CMA

[Mike Dewar]

Hi,

I've trained up a classifier using the (so-far wonderful) CMA package. It validated well, and gives me predictions that agree well with my labels. I'd now like to use the classifier on a held-out data set, but for the life of me I can't figure out how to apply a classifier to a new example. Does anyone have any ideas?

For example, having loaded my `exprset` and generated a `learning_set` using CMA's GenerateLearningsets(), I can run the classification() function as follows:

out = classification(
	X = t(exprs(exprset)), 
        y = pData(exprset)$labels, 
        learningsets = learning_set,
        classifier = rfCMA 
)

the object `out` gives me loads of information about how well it did and so on, but I can't seem to use "out" in order to classifiy a new set. An alternative approach would be to run something like classification() whereby I give it an X_test variable or something, but this doesn't seem to be available. 

Any help would be greatly appreciated : I'm sure I'm missing something basic!

Cheers,

Mike Dewar


- - -
Dr Michael Dewar
Postdoctoral Research Scientist 
Applied Mathematics
Columbia University
http://www.columbia.edu/~md2954/