[BioC] cycle package question

[Matthias Futschik]

Hi Alyaa,
as it is, the fdrfourier function accepts only expression set objects,
but with the conversion (ExpressionSet(matrix)), which you used, you
should be fine
also in cases where the matrix does not contain gene expression data,
as the fdrfourier uses the expression set object only as container for
the data matrix,
and does not utilize other features of the object.

hth,
Matthias. 

Em 17.09.2013 14:11, Steve Lianoglou escreveu:
> Hi,
>
> On Tue, Sep 17, 2013 at 5:54 AM, Alyaa Mahmoud <alyamahmoud at gmail.com> wrote:
>> its from the "cycle" package
>>
>> the function only accepts expression set object, so I originally wanted to
>> ask if its possible to change that
> I see -- if this is the case, you should cc the maintainer of the
> package who may not be watching these lists closely.
>
> I've have CC'd him (Matthias) here.
>
> HTH,
> -steve
>
>> so far, I have just converted the matrix into an expression set object
>> (ExpressionSet(matrix))
>>
>> but my original question was if its possible to pass a matrix directly to
>> the fdrfourier function because it can basically be used for any time
>> series dataset not necessarily expression dataset
>>
>> thanks a lot Steve for your reply
>>
>>
>> On Tue, Sep 17, 2013 at 3:50 PM, Steve Lianoglou
>> <lianoglou.steve at gene.com>wrote:
>>
>>> Hi,
>>>
>>> On Tue, Sep 17, 2013 at 2:21 AM, Alyaa Mahmoud <alyamahmoud at gmail.com>
>>> wrote:
>>>> Dear BioC group
>>>>
>>>> Is there a way we can apply the function fdrfourier to an expression
>>> matrix
>>>> directly and not necessarily an expressionSet object ?? Please advise
>>> I'm not aware of the `fdrfourrier` function (what package is it in?)
>>> but if you want to apply it on an ExpressionSet but the function
>>> itself only accepts a matrix and if `e` is your ExpressionSet, can't
>>> you just `fdrfourrier(exprs(e))`?
>>>
>>> -steve
>>>
>>> --
>>> Steve Lianoglou
>>> Computational Biologist
>>> Bioinformatics and Computational Biology
>>> Genentech
>>>
>>
>>
>> --
>> Alyaa Mahmoud
>>
>> "Love all, trust a few, do wrong to none"- Shakespeare
>>
>>         [[alternative HTML version deleted]]
>>
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>
>

-- 

************************************************************
Dr. Matthias E. Futschik
Principal Investigator in Systems Biology and Bioinformatics
Centre for Molecular and Structural Biomedicine
University of Algarve, Campus of Gambelas
8005-139 Faro, Portugal
url: www.sysbiolab.eu
email: mfutschik at ualg.pt
phone: + 351 289 244 403