Follow-up : one of my colleagues (who is not experiencing this problem)
noticed that I had an older version of impute than he did, so I have now
installed impute_1.22.0, but I still get the same error.

thanks,

Sheila


On Mon, May 24, 2010 at 3:01 PM, Sheila Reynolds <
sheilamoorereynolds@gmail.com> wrote:

>
> 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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