[BioC] Problems with MANOR and RSPerl

[Seth Falcon]

Hi James,

"James Morris" <james.morris at ucl.ac.uk> writes:

> Hello,
>
> I have been writing a script to run a MANOR analysis from perl script using 
> RSPerl
>
> I have created my arrayCGH object successfully I think but when I try and 
> evaluate this simple normalisation I get this error
>
> &R::eval("data(flags); local.spatial.flag$args <- alist(var = "LogRatio", 
> by.var = NULL, nk = 5, prop = 0.25, thr = 0.15, beta = 1, family = 
> "gaussian"); flag.list <- list(spatial = local.spatial.flag); array.norm <- 
> norm.arrayCGH(array, flag.list = flag.list, FUN = median, na.rm = TRUE)")
>
> Error in model.frame(formula, fownames, variables, varnames, extras, 
> extranames, :
>   invalid variable type
>
> this is R 2.2.1 on Mac OS X Server 10.3.9
>
> any ideas on what could be causing this would be great

That is a rather old version of R (and OS X) not to mention a rather
involved setup of calling R via Perl.

Have you tried to reproduce the error simply using R?  It would be
good to determine if this is an R issue or something particular to the
RSPerl interaction.

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org