No Robert, in my opinion you did the right thing.  You're right to expect
the replacement operation to do the right thing and it is a bug that it
doesn't work.

Kasper


On Fri, Jan 10, 2014 at 4:58 PM, Robert Castelo <robert.castelo@upf.edu>wrote:

> hi Kasper,
>
> you're right. i should have done this upfront, this was too much S4 magic
> to be true :)
>
> cheers,
> robert.
>
>
>
> On 1/10/14 5:14 PM, Kasper Daniel Hansen wrote:
>
>> Robert: The alternative to using exprs<- is to instantiate a new object,
>> just copying the old phenodata.
>>
>> Kasper
>>
>>
>> On Fri, Jan 10, 2014 at 10:58 AM, Levi Waldron <
>> levi.waldron@hunter.cuny.edu
>>
>>> wrote:
>>> On Fri, Jan 10, 2014 at 9:59 AM, Kasper Daniel Hansen <
>>> kasperdanielhansen@gmail.com> wrote:
>>>
>>>  Unfortunately, you may want to be careful about making it too robust
>>>> (depending on what you mean).  For example filtering methods could very
>>>> well be seen as replacing one matrix with a smaller one.  Not sure if
>>>> these
>>>> methods use exprs<-, but that is probably how I would do it.
>>>>
>>>> What would be better is if in the process of doing the replacement, the
>>>> other slots are harmonized in a relevant way.  That would require row
>>>> names
>>>> on the replacement matrix.
>>>>
>>>>  I suspect I also have used exprs<- to change the number of rows of an
>>> ExpressionSet during analyses, when there were no featureData. Not that I
>>> mind changing, but it may not be unusual "out there."
>>>
>>>
>>>          [[alternative HTML version deleted]]
>>
>>
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>
>

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