Re: [R] .gct file

From: Randy Johnson <rjohnson_at_ncifcrf.gov>
Date: Wed 20 Jul 2005 - 03:18:19 EST


If it is a text file ?read.table should provide enough details to read the file into R. Based on the file format referenced below it shouldn't be too hard to get at the parts you want.

Randy

On 7/19/05 1:06 PM, "Marc Schwartz (via MN)" <mschwartz@mn.rr.com> wrote:

> 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_file
> formats.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
>
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Randy Johnson
Laboratory of Genomic Diversity
NCI-Frederick
Bldg 560, Rm 11-85
Frederick, MD 21702
(301)846-1304


R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Wed Jul 20 03:24:23 2005

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