in this case since I could not figure out what went wrong I tried to transpose it in perl.
Certainly I understand your concern regarding handling numerical data in Perl. I read the file using read.csv, it
reads the original file very well. I am not using "-" as a field seperator. The data is too huge and
I need to check with my collaborators before I send it to out.
Many thanks for your comments.
Cheers ./Murli
Adaikalavan Ramasamy wrote:
See comments below.
On Fri, 2005-02-11 at 08:47 -0800, T. Murlidharan Nair wrote:
Thanks to all for trying to help me with problem. After spending a long time, I eventually solved it
by writing a perl script and transposing the matrix
If you plan on doing your analysis mostly in R, it would be best to use R directly. While perl is great for many things, I recommend caution with numerical data (e.g. it will happily add a character and a number)
Besides, you may risk extra computing overhead and debugging nightmares.
and re-reading the file. When I did this I got an
error saying I had duplicate row names (which in fact was not true or
How did you read the file ? e.g. read.delim, read.table, read.csv, ...
may be something to with
the naming conventions in R).
The column names were :
Wouldn't this become row names after you transpose it ? Nevermind, I have tested both cases below.
Tumor_VA_114-1, Tumor_VA_114-2,.....
But when I changed it to Tumor_VA_114_1, Tumor_VA_114_2 it worked fine.
I was not aware that - cannot be used to differentiate variables. Is this the case ?
Not true. I successfully read in (tab delimited) files containing either of the following contents in Redhat Fedora Core 3 and R-1.9.1 :
read.delim(file="file1.txt", row.names=1, header=TRUE) read.delim(file="file2.txt", row.names=1, header=TRUE)
----------------- File 1 --------------------- Index Tumor_VA_114-1 Tumor_VA_114-2 A 10 100 B 20 200 ----------------------------------------------
----------------- File 2 --------------------- Index Value Tumor_VA_114-1 100 Tumor_VA_114-2 200 ---------------------------------------------
Another possibility is that somehow you are using "-" as the field
separator.
Maybe some other software that use in between corrupted the dimnames ?
We can only guess since you have not provided neither a simple reproducible example, your operating system or working R version. Please read the posting guide first.
Sorry, if I wasted any of your time. Cheers ../Murli
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