[BioC] Limma -time course - no replicates

[Naomi Altman]

time=1:10
design=model.matrix(~time)



At 12:28 PM 6/8/2010, Lana Schaffer wrote:
>Naomi,
>Thanks.
>Can you give an example how to set up the design matrix?
>Lana
>
>________________________________________
>From: Naomi Altman [naomi at stat.psu.edu]
>Sent: Tuesday, June 08, 2010 7:49 AM
>To: Lana Schaffer; Naomi Altman; bioconductor at stat.math.ethz.ch
>Subject: Re: [BioC] Limma -time course - no replicates
>
>You can use LIMMA.  The key is to have time be a continuous variable,
>not a factor.  So time (or a function of time) is entered into the
>design matrix, instead of +/- 1 or 0.
>
>--Naomi
>
>At 02:11 AM 6/6/2010, Lana Schaffer wrote:
> >Naomi,
> >Can you please suggest a routine or software for us to use?
> >Lana
> >
> >________________________________________
> >From: Naomi Altman [naomi at stat.psu.edu]
> >Sent: Friday, June 04, 2010 6:49 PM
> >To: Lana Schaffer; bioconductor at stat.math.ethz.ch
> >Subject: Re: [BioC] Limma -time course - no replicates
> >
> >Only if you consider this to be a regression on a function of time,
> >instead of an ANOVA.
> >
> >--naomi
> >
> >At 07:12 PM 6/4/2010, Lana Schaffer wrote:
> > >Hi,
> > >We are trying to use Limma code for a Time Course Experiment without
> > >Replicates for 4 times.  From looking at the manual, looks like don't
> > >Need replicates.  But the ebayes routine complains about no residual
> > >Degrees of freedom.
> > >Can we use Limma for Time Course without replicates?
> > >Lana
> > >
> > >_______________________________________________
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> > >https://stat.ethz.ch/mailman/listinfo/bioconductor
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> >
> >Naomi S. Altman                                814-865-3791 (voice)
> >Associate Professor
> >Dept. of Statistics                              814-863-7114 (fax)
> >Penn State University                         814-865-1348 (Statistics)
> >University Park, PA 16802-2111
> >
> >_______________________________________________
> >Bioconductor mailing list
> >Bioconductor at stat.math.ethz.ch
> >https://stat.ethz.ch/mailman/listinfo/bioconductor
> >Search the archives:
> >http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>Naomi S. Altman                                814-865-3791 (voice)
>Associate Professor
>Dept. of Statistics                              814-863-7114 (fax)
>Penn State University                         814-865-1348 (Statistics)
>University Park, PA 16802-2111

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111