[Bioc-devel] If it looks like a duck, walks like a duck

[Martin Morgan]

Thanks! I've updated eSet initialize to coerce phenoData objects to
AnnotatedDataFrame and issue a warning.

Correct:

> obj <- new("ExpressionSet", phenoData=new("AnnotatedDataFrame"))
> obj <- new("ExpressionSet")

Incorrect, coerced to valid:

> obj <- new("ExpressionSet", phenoData=new("phenoData"))
Warning message:
updating phenoData argument to 'AnnotatedDataFrame' 
> validObject(obj)
[1] TRUE
 
Martin

Wolfgang Huber <huber at ebi.ac.uk> writes:

> Hi all,
>
> I guess I understand and approve the rationale behind this etc., but 
> still for a naive observer this error message might look silly -  is 
> there any chance we can make this look better:
>
> new("ExpressionSet", exprs = ex, phenoData = phenoData(a),
>    sampleNames = ...)
>
>
> Error in checkSlotAssignment(object, name, value) :
>         assignment of an object of class "phenoData" is not valid for 
> slot 'phenoData' in  an object of class "ExpressionSet"; is(value, 
> "AnnotatedDataFrame") is not TRUE
>
>
>
>
> ------------------------------------
>  > sessionInfo()
> Version 2.3.0 RC (2006-04-20 r37864)
> x86_64-unknown-linux-gnu
>
> attached base packages:
>   [1] "splines"   "grid"      "tools"     "methods"   "stats"     "graphics"
>   [7] "grDevices" "utils"     "datasets"  "base"
>
> other attached packages:
>   tilingArray  geneplotter     annotate   genefilter     survival 
>     vsn
>      "1.8.21"      "1.9.7"      "1.9.6"      "1.9.7"       "2.24" 
> "1.9.4"
>    colorspace  strucchange     sandwich          zoo RColorBrewer 
>    affy
>         "0.9"     "1.2-12"      "1.1-1"      "1.0-6"      "0.2-3" 
> "1.9.17"
>        affyio      Biobase     fortunes
>      "0.99.3"     "1.9.24"      "1.2-1"
>
>
> Best regards
>    Wolfgang
>
> -------------------------------------
> Wolfgang Huber
> European Bioinformatics Institute
> European Molecular Biology Laboratory
> Cambridge CB10 1SD
> England
> Phone: +44 1223 494642
> Fax:   +44 1223 494486
> Http:  www.ebi.ac.uk/huber
>
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