[BioC] covariance structures for limma

Gordon Smyth smyth at wehi.edu.au
Sat Apr 23 12:44:20 CEST 2005

>Date: Fri, 22 Apr 2005 16:12:43 -0600
>From: Jacob Michaelson <jjmichael at comcast.net>
>Subject: [BioC] covariance structures for limma
>To: bioconductor at stat.math.ethz.ch
>Hi All,
>With a *quick* search in the mailing list and through the limma PDF I
>couldn't find any information on how to provide for a covariance
>structure in limma (this is for a repeated measures experiment).  I
>know lme has "weights" and "correlation" arguments which should do the

There isn't any function called 'lme' in limma. Do you perhaps mean lmFit()?

>can anyone enlighten me on limma's way of specifying covariance

limma supports several different covariance structures: see sections on 
"technical replication", "within-array array replicate spots" and "separate 
channel analysis" in the User's Guide. You probably want the section on 
"technical replication". Only quite simple repeated measures designs are 


>Thanks in advance,
>Jake Michaelson

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