[R] .gct file

[Marc Schwartz (via MN)]

On Tue, 2005-07-19 at 12:28 -0400, Duncan Murdoch wrote:
> On 7/19/2005 12:10 PM, mark salsburg wrote:
> > 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

A quick Google search would suggest "Gene Cluster Text" file:

http://www.broad.mit.edu/cancer/software/genepattern/tutorial/gp_tutorial_fileformats.html#gct

produced by Gene Pattern:

http://www.broad.mit.edu/cancer/software/genepattern/

If correct, I would point Mark to the Bioconductor folks for more
information and assistance:

http://www.bioconductor.org/

HTH,

Marc Schwartz