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Question: cycle package question
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5.1 years ago by
Alyaa Mahmoud440
Alyaa Mahmoud440 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 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]]
modified 5.1 years ago • written 5.1 years ago by Alyaa Mahmoud440
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5.1 years ago by
Denali
Steve Lianoglou12k 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
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
0
5.1 years ago by
Alyaa Mahmoud440
Alyaa Mahmoud440 wrote:
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]]