Re: [R] .gct file

From: Spencer Graves <>
Date: Wed 20 Jul 2005 - 03:27:00 EST

          Try ?read.table or args(read.table). Might "skip=2" do what you want?

          spencer graves
p.s. I routinely "readLines(File, n=11)" to see how many headers there are AND identify the "sep" character. Then I "quantile(count.fields(File, ...))" to see if all records have the same number of fields. Then I call something like "read.table" with the appropriate arguments. Then I print the first 2 or so rows of the result to make sure I read the file correctly.

mark salsburg wrote:

> ok so the gct file looks like this:
> #1.2 (version number)
> 7283 19 (matrix size)
> Name Description Values
> .... ....... ......
> How can I tell R to disregard the first two lines and start reading
> the 3rd line in this gct file. I would just delete them, but I do not
> know how to open a gct. file
> thank you
> On 7/19/05, 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

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Spencer Graves, PhD
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Received on Wed Jul 20 03:38:57 2005

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