[BioC] silly question about read.table

[Naomi Altman]

If you look at the documentation for read.table, you will see a 
variable " colClasses".  You can use this to set each column to the 
correct type.

--Naomi

At 09:34 PM 2/24/2007, J.delasHeras at ed.ac.uk wrote:
>Quoting James Anderson <janderson_net at yahoo.com>:
>
> > I am trying to use pamr (prediction analysis of microarray), which
> > uses nearest shrunken centroid classification. Now I want to load my
> >  data using read.table, then use pamr. the codes are as follows:
> >
> > Training = read.table("A.txt",header = FALSE)
> > myData = list(x = Training,y = factor(TrainingLabel));
> > mytrain = pamr.train(myData)
> > It always complains "Error in x %*% Y : requires numeric
> > matrix/vector arguments"
> >
> > I think the main reason is variable Training read from read.table is
> >  an object, not just numeric matrix, I tried as.numeric(Training),
> > it  still has errors. I know if Training is created by something like
> >
> > Training = matrix(rnorm(1000*20),ncol=20)
> > It will not complain, since by this way, Training is purely a
> > numeric matrix, not object. Does anybody know how to convert the
> > object read from read.table to a pure numeric matrix?
> >
> > Thanks,
> >
> > James
>
>I am not familiar with pamr and the arguments it requires, but
>read.table will create a data frame object. As it has no header and
>(presumably) it only contains numbers in a table form, if you use
>'as.matrix(Training)' you'll convert Training from a data frame to a
>numeric matrix. If pamr expects a list where the first element is a
>matrix, it may work. Anyway, use 'as.matrix', not 'as.numeric'
>
>I hope this helps a bit!
>
>Jose
>
>--
>Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
>The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
>Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
>Swann Building, Mayfield Road
>University of Edinburgh
>Edinburgh EH9 3JR
>UK
>
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Naomi S. Altman                                814-865-3791 (voice)
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