From: Gavin Simpson <gavin.simpson_at_ucl.ac.uk>

Date: Mon, 03 Mar 2008 11:03:34 +0000

Date: Mon, 03 Mar 2008 11:03:34 +0000

The other respondants here have missed the point - write.table() as invoked by the OP does not produce a csv file. The default separator is " " (a space) in write.table(), so no wonder Excel cocked it up as it assumes that a csv file is one that has elements separated by a comma ",". We don't need to rely on extra packages or using Excel to fix-up the file written by R - just use R's tools appropriately.

Kei, some points.

Did you actually try to run the example you provided? It failed on line 4 for me as you use data.matrix as a name for an object and it is an R function, which R says can't be subset as data.matrix[x, ] in the call to apply.

Instead of being able to step through your code to see where the problem was I spent a few minutes trying to fix it up and decipher what you intended before I spotted the call to write.table.

Secondly, space out your code - it makes it much easier to read if you put spaces round "<-", e.g.:

x <- 1:20000

and leave a space after the "," comma separating arguments in function calls.

Now to the answer (or one possible answer)

To generate a proper csv file, see ?write.csv, or ?write.csv2 if you are in of those strange countries that uses a comma as the decimal separator. Because your example doesn't work, I can't test this, but this should give you a csv file that opens in Excel as you want:

write.csv(cbind(data[1], Variance=apply(data[,y], 1, var)),

file="c://variance.csv")

**HTH
**
G

On Sun, 2008-03-02 at 18:59 -0800, Keizer_71 wrote:

> Here is my R Code

*>
**> x<-1:20000
**> y<-2:141
**> data.matrix<-data.matrix(data[,y])#create data.matrix
**> variableprobe<-apply(data.matrix[x,],1,var)
**> variableprobe #output variance across probesets
**> hist(variableprobe) #displaying histogram of variableprobe
**> write.table(cbind(data[1],
**> Variance=apply(data[,y],1,var)),file='c://variance.csv')
**> #export as a .csv file.
**>
**> Output in Excel
**> all in 1 column.
**>
**> ProbeID "Variance"
**> 1 "224588_at" 21.5825745738848
**>
**> How do i separate them so that i can have three columns
**>
**> ProbeID Variance
**> 1 224588_at 21.582.....
**>
**> thanks,
**> Kei
**>
**>
*

-- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% ______________________________________________ R-help_at_r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.Received on Mon 03 Mar 2008 - 11:10:34 GMT

Archive maintained by Robert King, hosted by
the discipline of
statistics at the
University of Newcastle,
Australia.

Archive generated by hypermail 2.2.0, at Mon 03 Mar 2008 - 11:30:18 GMT.

*
Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help.
Please read the posting
guide before posting to the list.
*