[BioC] covariance structures for limma

[Gordon Smyth]

>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
>job...

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
>structures?

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 
supported.

Gordon

>Thanks in advance,
>
>Jake Michaelson