For tiling arrays, one often prefers to apply a different strategy for
preprocessing.

But if it's something you really want to do, you can extract the pms and do
it "manually":

pms = pm(xys)
pns = probeNames(xys)
res = basicRMA(pms, pns)

b


2014-02-19 20:25 GMT-03:00 James Yousin <yousin.james@gmail.com>:

> I am trying to do preprocessing on xys files and have used the
> pdInfoBuilder package to successfully build the annotation files,
> everything works until rma(), if I skip it I also get the results using
> ACME. But I would like to know why rma() didnt work with xys files.
>
>
> class(xys)
> [1] "TilingFeatureSet"
> attr(,"package")
> [1] "oligoClasses"
>
> rma(xys)
> Error in (function (classes, fdef, mtable) :
> unable to find an inherited method for function 'rma' for signature
> '"TilingFeatureSet"'
>
> is this happening because the object is not of any of the "ExonFeatureSet",
> "ExpressionFeatureSet", "GeneFeatureSet" or "SnpCnvFeatureSet".
>
> I do see elsewhere people got it to work on XYS files
>
> https://stat.ethz.ch/pipermail/bioconductor/2013-June/053378.html
>
> Thanks
>
> James
>
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