[BioC] Tiling array analysis, ACME problem

[adam_pgsql]

Hi,

I am looking for modules that can analyse overlapping tiling arrays (Agilent) used for expression studies. In testing ACME, the example in the documentation fails with this error:

[R 2.10.1, OSX 10.6.3]

> library(ACME)
> samps <- data.frame(SampleID = 1:3, Sample = paste("Sample", 1:3))
> dat <- matrix(rnorm(90000), nc = 3)
> colnames(dat) <- 1:3
> pos <- rep(seq(1, 10000 * 100, 100), 3)
> chrom <- rep(paste("chr", 1:3, sep = ""), each = 10000)
> annot <- data.frame(Chromosome = chrom, Location = pos)
> a <- new("aGFF", data = dat, annotation = annot, samples = samps)
> calc <- do.aGFF.calc(a, window = 1000, thresh = 0.95)
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "chromosome", for signature "aGFF"

Am I missing something?

also are there any other modules in common use for Tiling array analysis?

thanks for any help

adam