[R] sample

[T. Murlidharan Nair]

My R version s 2.0.1 and I am running it under windows. I want to use R 
directly, but
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
>>
>>    
>>