[NMF-user] Resolved Error

[Jeffrey Herbstman]

Renaud asked me to post this to the list after an e-mail exchange:

I was wondering if you might be able to help me implement the 'NMF' R package that you wrote.  I'm trying to run through the example in the r-forge vignette, but I keep running into an error. It looks like it has something to do with the fact I'm trying to use an ExpressionSet, rather than a matrix. The simple as.matrix(esGolub) command doesn't seem to work for ExpressionSet types.

My code is pasted below. Any help would be great. Thanks!

> data(esGolub)
> esGolub <- esGolub[1:200, ]
> esGolub$Sample <- NULL
> res <- nmf(esGolub, 3)
Error in function (classes, fdef, mtable)  : 
 unable to find an inherited method for function ‘nmf’ for signature ‘"ExpressionSet", "numeric", "missing"’
> esMat <- as.matrix(esGolub)
Error in as.vector(data) : 
 no method for coercing this S4 class to a vector

I did not have BioBase installed when first installing the NMF package. After re-installing NMF and adding the extras (install.extras('NMF')), it solved the problem. 

Best,

Jeff