[Bioc-devel] RFC: read.AnnotatedDataFrame

Wolfgang Huber huber at ebi.ac.uk
Thu May 24 16:56:17 CEST 2007

Hi Martin,

> There have been a couple of requests for widget support, so
> implementing rather than removing the widget option might be better
> (though of course more difficult -- there are several different paths
> through the code, users haven't been forthcoming about which are
> actually important to them, and different paths have different sets of
> bugs / design issues that make adoption to AnnotatedDataFrame more
> challenging than you might expect).

Frankly, if people can prepare a file easily with MS Excel and then call
a simple function to read it into R, I do not see much of a use case for
a widget. Anyway, I am not in a position to implement the widgets
functionality, but if it turns out that someone is, maybe this would be
something for the wonderful new Qt stuff rather than tcltk?

Currently, the outcome of using this option with read.AnnotatedDataFrame
and read.AnnotatedDataFrame2 results in the same: an error. But we can
keep it around in the function signature if it makes people happier :)

> Along the same lines, the args to read.AnnotatedDataFrame were copied
> from read.phenoData; probably there are a number of scripts out there
> relying on these.

Hmm, but read.phenoData is a different function than
read.AnnotatedDataFrame. Is your design goal that one should be able to
simply replace all calls to read.phenoData in existing scripts with
calls to read.AnnotatedDataFrame? I think people that move their scripts
from exprSet to ExpressionSet are in for some refactoring anyway, and I
think (but of course may be wrong) that the new defaults would make more
people happier in the long term.

Ideally, this function would be one of the first that new users of
Bioconductor learn e.g. in a lab or in a vignette, that's the reason why
I am a bit sceptical of exposing them to all the wonderful options of
read.table straight away (as is done now e.g. in the man page of

 Best wishes

> Wolfgang Huber <huber at ebi.ac.uk> writes:
>> Dear all,
>> I have a checked in a new function read.AnnotatedDataFrame2 into Biobase 
>> (>= 1.15.12), which has (somewhat) different arguments from the existing 
>> read.AnnotatedDataFrame:
>> - different defaults for the  read.table options:
>>     sep="\t", header=TRUE, quote ="", as.is=TRUE,
>> - no 'widget' argument (which is anyway unimplemented).
>> A nice feature is that the new function allows more easily to specify 
>> the varMetadata.
>> Ideally, I would like read.AnnotatedDataFrame2 to replace the existing 
>> read.AnnotatedDataFrame, but for this would like to request your 
>> feedback: is anyone very attached to the function 
>> read.AnnotatedDataFrame in its current form? Would changing its API 
>> break lots of things? Please speak up if "yes", otherwise I might 
>> interpret that as "no".
>> Best wishes
>>    Wolfgang
>> ------------------------------------------------------------------
>> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
>> _______________________________________________
>> Bioc-devel at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

Best wishes

Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

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