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
Looking forward to your reply
Thanks a lot
yours,
Alyaa Mahmoud
--
Alyaa Mahmoud
"Love all, trust a few, do wrong to none"- Shakespeare
[[alternative HTML version deleted]]
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
its from the "cycle" package
the function only accepts expression set object, so I originally
wanted to
ask if its possible to change that
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>wrote:
> Hi,
>
> On Tue, Sep 17, 2013 at 2:21 AM, Alyaa Mahmoud
<alyamahmoud@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]]
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]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
--
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech
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]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
--
************************************************************
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
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]]
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@r-project.org <javascript:;>
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> >
>
> --
>
> ************************************************************
> 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
[[alternative HTML version deleted]]
