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
> >>>>
> >>>>______________________________________________
> >>>>[email protected] 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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> >>>https://stat.ethz.ch/mailman/listinfo/r-help
> >>>PLEASE do read the posting guide!
> >>>
> >>>
> >>http://www.R-project.org/posting-guide.html
> >>
> >>
> >>______________________________________________
> >>[email protected] 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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