I am trying to use a new (to me) package (samr) and even when I try to run a
very simple example, I get this "cannot open the connection" error.
The reason I am writing to r-help rather than to the authors of samr is I
think this may be a more general R problem rather than a samr-specific
problem. Perhaps something with my installation and write access to some
particular place ? I am currently running on a Windows box (where I do not
have administrator privileges) but have been meaning to shift over to a
linux box, perhaps this will push me there faster.
In any case, if anyone has a suggestion on where I should look to solve
this, I'd greatly appreciate it. Below is what I tried and what happened
(with the error highlighted in bold red font).
thanks in advance,
Sheila
> library (samr)
Loading required package: impute
>
> ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-
> ## testing the two class unpaired example from the man pages ...
>
> set.seed(100)
> x <- matrix ( rnorm(1000*20), ncol=20 )
> dd <- sample ( 1:1000, size=100 )
> u <- matrix ( 2*rnorm(100), ncol=10, nrow=100 )
> x[dd,11:20] <- x[dd,11:20] + u
> y <- c(rep(1,10),rep(2,10))
>
> data <- list ( x=x, y=y, geneid=as.character(1:nrow(x)),
+ genenames=paste("g",as.character(1:nrow(x))) )
>
> samr.obj <- samr ( data, resp.type="Two class unpaired",
+ nperms=100, logged2=TRUE )
Error in samr(data, resp.type = "Two class unpaired", nperms = 100, logged2
= TRUE) :
unused argument(s) (logged2 = TRUE)
Error during wrapup: cannot open the connection
>
>
> samr.obj <- samr ( data, resp.type="Two class unpaired",
+ nperms=100 )
perm= 1
Error in !logged2 : invalid argument type
*Error during wrapup: cannot open the connection*
> sessionInfo()
R version 2.11.0 (2010-04-22)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] samr_1.28 impute_1.0-5
>
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