On Mon, Nov 14, 2011 at 7:37 AM, Bas Jansen <bjhjansen@gmail.com> wrote:

> Hi Bioconductor gurus:
>
> I am trying to make ExpressionSet files for the analysis of PCR
> arrays, to be able to analyze them in LMGene. However, I get the
> following error message:
>
> > eSet_xxx <- new("ExpressionSet", exprs = exprs_xxx, phenoData =
> phenoData_xxx, experimentData = experimentData)
> Error in function (classes, fdef, mtable)  :
>  unable to find an inherited method for function
> "annotatedDataFrameFrom", for signature "data.frame"
>
> I have done this a gazillion times before without a hitch, and
> suddenly I'm not able to do so anymore. If anyone knows what's going
> on, I am all ears.
>
> Dear Bas,

Did you have a look at documentation?   There is a vignette in Biobase
called BiobaseDevelopment that shows that we pass an AnnotatedDataFrame
instance in for phenoData.

obj <- new("ExpressionSet", phenoData = new("AnnotatedDataFrame"),
experimentData = new("MIAME"), annotation = character(), exprs =
new("matrix"))

You don't say what class phenoData_xxx has, but presumably it is a
data.frame.  The following may be relevant

> new("AnnotatedDataFrame", data=data.frame())
An object of class "AnnotatedDataFrame": none
> new("AnnotatedDataFrame", data=data.frame(1))
An object of class "AnnotatedDataFrame"
  rowNames: 1
  varLabels: X1
  varMetadata: labelDescription



> Kind regards,
> Bas
>
> > sessionInfo()
> R version 2.13.2 (2011-09-30)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C/UTF-8/C/C/C/C
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
> [1] LMGene_2.8.0     affy_1.30.0      survival_2.36-10 multtest_2.8.0
> [5] Biobase_2.12.2
>
> loaded via a namespace (and not attached):
> [1] MASS_7.3-14           affyio_1.20.0         preprocessCore_1.14.0
> [4] tcltk_2.13.2
>
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