[BioC] Limma -time course - no replicates

Naomi Altman naomi at stat.psu.edu
Tue Jun 8 16:49:27 CEST 2010

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.


At 02:11 AM 6/6/2010, Lana Schaffer wrote:
>Can you please suggest a routine or software for us to use?
>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.
>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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>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
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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

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