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??
thank you.
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
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 MurdochA 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
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 <murdoch at stats.uwo.ca> 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 >
On 7/19/2005 1:16 PM, 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. fileUse skip=2. See ?read.table. Duncan Murdoch
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 <murdoch at stats.uwo.ca> 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 >> > > > ______________________________________________ > R-help at 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-- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA spencer.graves at pdf.com www.pdf.com <http://www.pdf.com> Tel: 408-938-4420 Fax: 408-280-7915