Hi all,
I want to simulate counts for 1000 genes for 5 RNA-seq samples (with 3
biological replicates each), and I want to provide the dispersion
parameters myself.
Is there a package or code that can help me do this?
Thanks a lot for your help,
Al
[[alternative HTML version deleted]]
I should mention I want to use negative binomial as underlying
distribution.
Thanks.
Al
On Tue, Aug 21, 2012 at 9:41 AM, Alpesh Querer <alpeshq@gmail.com>
wrote:
> Hi all,
>
> I want to simulate counts for 1000 genes for 5 RNA-seq samples (with
3
> biological replicates each), and I want to provide the dispersion
> parameters myself.
> Is there a package or code that can help me do this?
>
> Thanks a lot for your help,
> Al
>
[[alternative HTML version deleted]]
You could start with rnbinom(). The 'size' argument is 1/dispersion.
Mark
On 21.08.2012, at 16:51, Alpesh Querer wrote:
> I should mention I want to use negative binomial as underlying
distribution.
>
> Thanks.
> Al
>
> On Tue, Aug 21, 2012 at 9:41 AM, Alpesh Querer <alpeshq at="" gmail.com=""> wrote:
>
>> Hi all,
>>
>> I want to simulate counts for 1000 genes for 5 RNA-seq samples
(with 3
>> biological replicates each), and I want to provide the dispersion
>> parameters myself.
>> Is there a package or code that can help me do this?
>>
>> Thanks a lot for your help,
>> Al
>>
>
> [[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
----------
Prof. Dr. Mark Robinson
Bioinformatics
Institute of Molecular Life Sciences
University of Zurich
Winterthurerstrasse 190
8057 Zurich
Switzerland
v: +41 44 635 4848
f: +41 44 635 6898
e: mark.robinson at imls.uzh.ch
o: Y11-J-16
w: http://tiny.cc/mrobin
----------
http://www.fgcz.ch/Bioconductor2012http://www.eccb12.org/t5
Try FluxSimulator, or BEERS, both mentioned in this thread:
http://seqanswers.com/forums/showthread.php?t=5386
-Aaron
On Tue, Aug 21, 2012 at 11:00 AM, Mark Robinson
<mark.robinson@imls.uzh.ch>wrote:
>
> You could start with rnbinom(). The 'size' argument is
1/dispersion.
>
> Mark
>
> On 21.08.2012, at 16:51, Alpesh Querer wrote:
>
> > I should mention I want to use negative binomial as underlying
> distribution.
> >
> > Thanks.
> > Al
> >
> > On Tue, Aug 21, 2012 at 9:41 AM, Alpesh Querer <alpeshq@gmail.com>
> wrote:
> >
> >> Hi all,
> >>
> >> I want to simulate counts for 1000 genes for 5 RNA-seq samples
(with 3
> >> biological replicates each), and I want to provide the dispersion
> >> parameters myself.
> >> Is there a package or code that can help me do this?
> >>
> >> Thanks a lot for your help,
> >> Al
> >>
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> ----------
> Prof. Dr. Mark Robinson
> Bioinformatics
> Institute of Molecular Life Sciences
> University of Zurich
> Winterthurerstrasse 190
> 8057 Zurich
> Switzerland
>
> v: +41 44 635 4848
> f: +41 44 635 6898
> e: mark.robinson@imls.uzh.ch
> o: Y11-J-16
> w: http://tiny.cc/mrobin
>
> ----------
> http://www.fgcz.ch/Bioconductor2012
> http://www.eccb12.org/t5
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
[[alternative HTML version deleted]]
There is also
DESeq::makeExampleCountDataSet
in the DESeq package. You could modify the function which currently
doesn't
contain any input args for the number of genes, biological replicates
or
pi0, proportion of truely null hypotheses.
Marcus
On Wed, Aug 22, 2012 at 5:28 AM, Aaron Mackey <amackey@virginia.edu>
wrote:
> Try FluxSimulator, or BEERS, both mentioned in this thread:
>
> http://seqanswers.com/forums/showthread.php?t=5386
>
> -Aaron
>
> On Tue, Aug 21, 2012 at 11:00 AM, Mark Robinson
> <mark.robinson@imls.uzh.ch>wrote:
>
> >
> > You could start with rnbinom(). The 'size' argument is
1/dispersion.
> >
> > Mark
> >
> > On 21.08.2012, at 16:51, Alpesh Querer wrote:
> >
> > > I should mention I want to use negative binomial as underlying
> > distribution.
> > >
> > > Thanks.
> > > Al
> > >
> > > On Tue, Aug 21, 2012 at 9:41 AM, Alpesh Querer
<alpeshq@gmail.com>
> > wrote:
> > >
> > >> Hi all,
> > >>
> > >> I want to simulate counts for 1000 genes for 5 RNA-seq samples
(with 3
> > >> biological replicates each), and I want to provide the
dispersion
> > >> parameters myself.
> > >> Is there a package or code that can help me do this?
> > >>
> > >> Thanks a lot for your help,
> > >> Al
> > >>
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor@r-project.org
> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> > ----------
> > Prof. Dr. Mark Robinson
> > Bioinformatics
> > Institute of Molecular Life Sciences
> > University of Zurich
> > Winterthurerstrasse 190
> > 8057 Zurich
> > Switzerland
> >
> > v: +41 44 635 4848
> > f: +41 44 635 6898
> > e: mark.robinson@imls.uzh.ch
> > o: Y11-J-16
> > w: http://tiny.cc/mrobin
> >
> > ----------
> > http://www.fgcz.ch/Bioconductor2012
> > http://www.eccb12.org/t5
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
[[alternative HTML version deleted]]
