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?
>

Yes, but that is my fault.  As of the version of ACME that you are likely
using (I can't tell because there is no sessionInfo()), the recommended data
structure is the ACMESet rather than an aGFF.  This data structure is what
is used in the vignette.  However, the do.aGFF.calc help is INCORRECT and
the "x" argument should be an ACMESet object.  So, working through your
example (and thanks for the nice, reproducible example):

samps <- data.frame(SampleID = 1:3, Sample = paste("Sample",
1:3),row.names=1:3)
dat <- matrix(rnorm(90000), nc = 3)
colnames(dat) <- 1:3
starts <- rep(seq(1, 10000 * 100, 100), 3)
ends <- starts +50 # ACMESet needs ends, also, but could be equal to starts
chrom <- rep(paste("chr", 1:3, sep = ""), each = 10000)
a <- new("ACMESet",exprs=dat,
    phenoData=as(samps,"AnnotatedDataFrame"),

 featureData=as(data.frame(chromosome=chrom,start=starts,end=ends),"AnnotatedDataFrame"))
calc = do.aGFF.calc(a,window = 1000, thresh = 0.95)

I will fix the documentation to make things clearer.  Sorry for the
confusion.


>
> also are there any other modules in common use for Tiling array analysis?
>
>
Not sure about common use, but check tilingArray, among others?

Sean

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