[BioC] Error while building ExpressionSet from scratch....

[Martin Morgan]

On 11/14/2011 04:37 AM, Bas Jansen 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"

you're not providing a featureData instance, so R is trying to infer one 
from exprs. My guess is that exprs is data.frame, but should be a matrix.

In R-2.14 there is the function ExpressionSet() which might make this 
more transparent

 > args(ExpressionSet)
function (assayData, phenoData = annotatedDataFrameFrom(assayData,
     byrow = FALSE), featureData = annotatedDataFrameFrom(assayData,
     byrow = TRUE), experimentData = new("MIAME"), annotation = 
character(),
     protocolData = annotatedDataFrameFrom(assayData, byrow = FALSE),
     ...)
NULL

Martin

>
> 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.
>
> 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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