Great, thanks a lot for your reply

On Tuesday, September 17, 2013, Matthias Futschik wrote:

> 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@gmail.com<javascript:;>>
> 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@gene.com <javascript:;>>wrote:
> >>
> >>> Hi,
> >>>
> >>> On Tue, Sep 17, 2013 at 2:21 AM, Alyaa Mahmoud <alyamahmoud@gmail.com<javascript:;>
> >
> >>> 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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> >> Bioconductor@r-project.org <javascript:;>
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> >> Search the archives:
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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@ualg.pt <javascript:;>
> phone: + 351 289 244 403
> ************************************************************
>
>

-- 
Alyaa Mahmoud

"Love all, trust a few, do wrong to none"- Shakespeare

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