[R] reading tables into R

[Wagle, Mugdha]

I have been using R and Perl. When  I read in a text file using the read.table option, and I try to mathematically manipulate the individual elements in the table, I keep getting an "object is not subsettable" error. If I try to use a different method, it works, but takes too much time(basically, I then need to read in values individually into R instead of as a 2D array, so the number of function calls from Perl to R is very large). Could you suggest another method whereby I could read an entire matrix or a file using an R function call? 
 
Thanks!
 
Sincerely,
Mugdha Wagle,
Hartwell center for Bioinformatics and Biotechnology,
St.Jude Children's Research Hospital