.gct file

I have two files to compare, one is a regular txt file that I can read
in no prob.

The other is a .gct file (How do I read in this one?)

I tried a simple

read.table("data.gct", header = T)

How do you suggest reading in this file??

.gct is not a standard filename extension.  You need to know what is in 
that file.  Where did you get it?  What program created it?

Chances are the easiest thing to do is to get the program that created 
it to export in a well known format, e.g. .csv.

Duncan Murdoch