[Bioc-devel] Error handling in AnnotatedDataFrames

[Martin Morgan]

On 12/16/2010 09:47 AM, Simon Anders wrote:
> Hi,
> 
> These AnnotatedDataFrames are driving me nuts. Somehow, I always stumble

I checked in code to devel (Biobase 2.11.7) that says

> adf <- new("AnnotatedDataFrame", data.frame(a=1:5))
> varMetadata(adf)["a", "labelDescription"] <- "foo"
> varMetadata(adf)["b", "labelDescription"] <- "foo"
Error in `varMetadata<-`(`*tmp*`, value = list(labelDescription =
c("foo",  :
  'b' not in 'varLabels(<AnnotatedDataFrame>)'

Martin

> over unexpected behaviour.
> 
> Here is a test case, resulting in an error mesage, that just managed to
> severely confuse me:
> 
> Let's make an AnnotatedDataFrame with two columns, called 'a' and 'b'.
> 
>> adf <- new("AnnotatedDataFrame",
> +   data=data.frame( a = 1:10, b = 11:20 ) )
> 
> Document the first column:
> 
>> varMetadata( adf )[ "a", "labelDescription" ] <- "a column named 'a'"
> 
> Now, I try to document the second column, but misspell its name as 'c'
> instead of 'b'. Let's see how this error is reported:
> 
>> varMetadata( adf )[ "c", "labelDescription" ] <-
> +    "a column that does not exist"
> Error in `row.names<-.data.frame`(`*tmp*`, value = c("a", "b")) :
>   invalid 'row.names' length
> 
> From this error message, it is quite hard to guess the cause of the
> error. Could somebody who is more familiar with the internals of Biobase
> maybe have a look whether this error condition could be caught earlier
> to give a more helpful error?
> 
> Cheers
>   Simon
> 
> 
> 
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
>  [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>  [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
>  [7] LC_PAPER=en_US.utf8       LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] ExonSeq_0.1.0  MASS_7.3-8     Biobase_2.10.0
> 
> loaded via a namespace (and not attached):
> [1] hwriter_1.3  tools_2.12.0
> 
> 
> 
> +---
> | Dr. Simon Anders, Dipl.-Phys.
> | European Molecular Biology Laboratory (EMBL), Heidelberg
> | office phone +49-6221-387-8632
> | preferred (permanent) e-mail: sanders at fs.tum.de
> 
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


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