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 Thanks James Morris

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