[BioC] spline example from limma user's guide

[Paul Geeleher]

For repeated measures of the same individual you will want to include
an identified as a factor in the model.

Eg. where there are 2 patients "p1" and "p2".

ids <- factor(c("p1", "p1", "p1", "p2", "p2", "p2"))
design <- model.matrix(~yourExistingModel+ids)

Paul.


On Tue, Apr 16, 2013 at 2:10 PM, Juliet Hannah <juliet.hannah at gmail.com> wrote:
> All,
>
> In section 8.6.2 of the limma user's guide, an example is given using
> splines for time-course data. It looks like in this example, the data
> points are independent, meaning different subjects are observed at
> different timepoints.
>
> If the same subject is observed over time, is it correct to use
> duplicateCorrelation function along with the spline model. Is this the
> correct way to handle profiles of individuals in limma?
>
> What other Bioconductor approaches have people used? I can't tell if EDGE
> (Leek and colleagues) is updated/maintained.
>
> Thanks,
>
> Juliet
>
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>
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-- 
Dr. Paul Geeleher, PhD (Bioinformatics)
Section of Hematology-Oncology
Department of Medicine
The University of Chicago
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