[BioC] Inherits(x,"data.frame") error in SamR

[Seth Falcon]

Hi Monnie,

I have a few suggestions, but as I haven't used the functions you want
to use I'm not certain they will help.

First, if what you want is to get a hold of the expression matrix in
the exprSet, you do not need to convert to data.frame first.  

Instead of this:
> gs.rma.fr = as.data.frame.exprSet(gs.rma)
> gs.mat = matrix(gs.rma.fr$exprs,nrow=14010,ncol=6)

Try: gs.mat = exprs(gs.rma)

The error msg you saw:

    > samr(data,resp.type="Two class unpaired",nperms=20)
    Error in inherits(x, "data.frame") : (subscript) logical subscript
    too long

seems to suggest that samr is expecting a data.frame, not a list.
They are similar, but not the same.  So you might try:

   data = data.frame(x=gs.mat.sam, y=y , geneid = geneid, 
                     genenames=rep(genenames,2), logged2=TRUE)

HTH,

+ seth