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On Tue, Jun 1, 2010 at 9:11 AM, adam_pgsql <adam_pgsql@witneyweb.org> wrote:

>
> 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
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