read.table

I am using read.table() to read in ASCII data into a data
frame.  The file has multiple columns that are not the
same length.  The function gives me errors, or I get 'NA'
characters in the blank fields.  I want to read these values
in to, e.g., perform a two-sample t-test.

You can't use read.table.  It is designed to read a data frame where by 
definition the columns are the same length.

What you can do is to use scan and remove the NAs as in

tmp <- lapply(scan("foo.txt", list(0, 0)), function(x) x[!is.na(x)])

which will give you a list of two numeric vectors.

Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595