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

Wolfgang Huber huber at ebi.ac.uk
Thu Apr 20 16:23:07 CEST 2006

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)

attached base packages:
  [1] "splines"   "grid"      "tools"     "methods"   "stats"     "graphics"
  [7] "grDevices" "utils"     "datasets"  "base"

other attached packages:
  tilingArray  geneplotter     annotate   genefilter     survival 
     "1.8.21"      "1.9.7"      "1.9.6"      "1.9.7"       "2.24" 
   colorspace  strucchange     sandwich          zoo RColorBrewer 
        "0.9"     "1.2-12"      "1.1-1"      "1.0-6"      "0.2-3" 
       affyio      Biobase     fortunes
     "0.99.3"     "1.9.24"      "1.2-1"

Best regards

Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber

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