[R] sample

Sat Feb 12 02:36:50 CET 2005

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
> 
> 
> 
> Liaw, Andy wrote:
> 
> >?sample says:
> >
> >x   Either a (numeric, complex, character or logical) vector of more
> >    than one element from which to choose, or a positive integer 
> >
> >so I guess it wasn't meant to be used on a data frame.  However, a data
> >frame is a list (where the variables are the components), and a list is a
> >vector, so the behavior is consistent:
> >
> >  
> >
> >>x <- list("a", 2, "c", 4, "e", "f")
> >>sample(x)
> >>    
> >>
> >[[1]]
> >[1] "c"
> >
> >[[2]]
> >[1] "a"
> >
> >[[3]]
> >[1] 4
> >
> >[[4]]
> >[1] 2
> >
> >[[5]]
> >[1] "f"
> >
> >[[6]]
> >[1] "e"
> >
> >Andy
> >
> >  
> >
> >>From: Jean Eid
> >>
> >>It seems that sample picks columns when the object is turned into a
> >>data.frame. I do not knoe why it is doing that....
> >>
> >>Is this something that was meant and not documented or something?
> >>
> >>
> >>Jean
> >>
> >>
> >>On Fri, 11 Feb 2005, Adaikalavan Ramasamy wrote:
> >>
> >>    
> >>
> >>>See below.
> >>>
> >>>On Thu, 2005-02-10 at 14:53 -0800, T. Murlidharan Nair wrote:
> >>>      
> >>>
> >>>>Just to explain my previous mail, here is the output I get.
> >>>>
> >>>>
> >>>> > dim(tissue.exp)
> >>>>[1] 1532   20
> >>>>        
> >>>>
> >>>What is this object ? Try class(tissue.exp)
> >>>
> >>>      
> >>>
> >>>> > pick<-sample(tissue.exp,5,replace=TRUE)
> >>>> > dim(pick)
> >>>>[1] 1532    5
> >>>>        
> >>>>
> >>>>From help(sample) :
> >>>
> >>>    sample(x, size, replace = FALSE, prob = NULL)
> >>>
> >>>    x: Either a (numeric, complex, character or logical) vector of
> >>>       more than one element from which to choose, or a positive
> >>>       integer.
> >>>
> >>>x has to be a vector or positive integer integer. I am not 
> >>>      
> >>>
> >>sure how you
> >>    
> >>
> >>>got "sample" to work on tissue.exp in the first place. Maybe you got
> >>>your own version of "sample".
> >>>
> >>>
> >>>      
> >>>
> >>>> > tissue.exp.t<-t(tissue.exp)
> >>>> > dim(tissue.exp.t)
> >>>>[1]   20 1532
> >>>> > pick<-sample(tissue.exp.t,5,replace=TRUE)
> >>>> > dim(pick)
> >>>>NULL
> >>>>
> >>>>--------
> >>>>Thanks ../Murli
> >>>>
> >>>>______________________________________________
> >>>>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
> >>    
> >>
> >>>      
> >>>
> >>______________________________________________
> >>    
> >>
> >>>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
> >>    
> >>
> >>______________________________________________
> >>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
> >>
> >>
> >>    
> >>
> >
> >
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