[Bioc-devel] [biocpkgs] Bug? in AssayData

[Seth Falcon]

"Oosting, J. (PATH)" <J.Oosting at lumc.nl> writes:
> My issue is with assayDataElementNames(), I just stumbled across
> assayDataElement when I checked an error that popped up recently.
>
> I have an eSet subclass that has optional elements in assayData
>
> I use something like if ( !("intensity" %in%
> assayDataElementNames(object))) object<-CalculateIntensity(object)
>
>
> When the object has storageMode=="list" I get an error, because the
> function assayDataStorageMode tests this assuming the argument is an
> AssyData instance, but the following commands in the function assume
> this is an eSet instance.
>
>> assayDataElementNames <- function(obj)   if
>> (assayDataStorageMode(obj) == "list") names(assayData(obj)) else
>> ls(assayData(obj))
>
> This should either be: if (assayDataStorageMode(assayData(obj)) ==
> "list") or if (storageMode(obj) == "list")

I agree there is ambiguity here that needs fixing.  Thanks for
clarifying the issues you encountered.

We will have some discussion among the developers here and have some
sort of a fix posted asap.

My initial feeling is that much of this code would be less confusing
if these were methods and not functions.  

Best,

+ seth