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
>
>
--
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
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