[BioC] repeated measures in limma?

[michael watson (IAH-C)]

Hi Rob

If memory serves me right, limma thinks all replicates are biological replicates, and one can specify technical replicates using the block argument... I think... it's all in the UserGuide that I don't have with me at the moment, but if you open up the PDF and search for "technical replicate" you should find the relevant section.

Mick


-----Original Message-----
From:	bioconductor-bounces at stat.math.ethz.ch on behalf of rob foxall (IFR)
Sent:	Thu 10/11/2005 11:42 AM
To:	bioconductor at stat.math.ethz.ch
Cc:	
Subject:	[BioC] repeated measures in limma?
Hi,
	My problem is as follows: I have a bunch of subjects with a
medical condition, and a bunch of normals, and I am looking for
differences between the two groups. However, I have several arrays per
subject (biological replicates), and so would like to include subject
variability into the model. If this was a usual single-response problem,
I might use the package "nlme" from R, something like

fit <- lme(fixed=response ~ condition, data=mydata, random= ~1 |
Subject)

Is there something analogous to this in limma?

Cheers,
	Rob.

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