On 2013-02-20 22:02, Hervé Pagès wrote:
Hi Robert,
Nice to hear from you!
I'm just a little bit worried that if we put normalize() in
BiocGenerics without at the same time have a "take it or leave it"
policy, then most of the authors of the 10 packages are likely going
to ignore that there is n
On 02/20/2013 01:02 PM, Hervé Pagès wrote:
...
Furthermore, the good citizens that modify their package to use the
normalize() in BiocGenerics will be in a situation worth than before
because, from an end user point of view, their normalize() function
(which is now a method attached to BiocGeneri
Hi Robert,
Nice to hear from you!
I'm just a little bit worried that if we put normalize() in
BiocGenerics without at the same time have a "take it or leave it"
policy, then most of the authors of the 10 packages are likely going
to ignore that there is now a new normalize() in BiocGenerics. The
my 2c worth
On Wed, Feb 20, 2013 at 10:45 AM, Hervé Pagès wrote:
> Hi,
>
> I agree with Laurent that we can't really play the semantic and concept
> police. It's the responsibility of package authors to decide whether
> it's appropriate or not to call "normalization" that particular
> transformat
Dear all,
Looking at the alphabetical list of functions/methods in BioGenerics I
have the feeling that all functions are really generic, i.e. general,
with the exception of function 'annotation' which in my opinion should
be part of BioBase as method for one or more of the BioBase classes.
T
Hi Laurent, LEo
there is a clash between two concepts, which seem difficult & messy to
reconcile, and all I wanted to do with my initial post was to spur an explicit
discussion and awareness of this, rather than just doing it implicitly. Not yet
sure if that is going to be productive.
1. packa
Hi,
I agree with Laurent that we can't really play the semantic and concept
police. It's the responsibility of package authors to decide whether
it's appropriate or not to call "normalization" that particular
transformation they're implementing.
However I hope that we all agree on the following
On 2013-02-20 17:32, Schalkwyk, Leonard wrote:
Is this not just an indication that normalize is now a poor choice of a
function name?
If the package authors called the functions "normalize", this means either:
1- at least some of the package authors have named a function performing
an action
Is this not just an indication that normalize is now a poor choice of a
function name?
LEo
On 20 Feb 2013, at 16:14, Wolfgang Huber wrote:
> Hi
>
> is it clear that all these different functions (methods) share similar
> semantics and enough (conceptually) of their interface?
>
> Wouldn't
Hi
is it clear that all these different functions (methods) share similar
semantics and enough (conceptually) of their interface?
Wouldn't the implication be that preemptively every possible string of
characters should already be defined as a generic function in BiocGenerics?
Best wish
On 19 February 2013 22:44, Hervé Pagès wrote:
> Hi Laurent, and maintainers of packages with a normalize() function,
>
>
> On 02/15/2013 04:28 AM, Laurent Gatto wrote:
>>
>> A quick (and incomplete) manual search using
>> http://search.bioconductor.jp/ suggest the following usage of
>> normalize:
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