[BioC] covariance structures for limma

Jacob Michaelson jjmichael at comcast.net
Sat Apr 23 22:54:59 CEST 2005

On Apr 23, 2005, at 4:44 AM, Gordon Smyth wrote:

>> 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()?

Actually I was just referring to lme() in the nlme package...

>> 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.

Thanks for the tip.  I'll check it out...As an aside, are there any 
plans to support more complex repeated measures designs in the future?  
I know Bioconductor traditionally has covered more medicine-centric 
microarray experiments (where repeated meaures analysis doesn't come up 
too often), but being at an agricultural university with a new Affy 
core lab, I anticipate many more microbial and plant arrays with 
repeated measures designs.  Fleshing out the repeated measures analysis 
capabilities in any BioC pacakge would be *very* helpful for current 
and future research as more and more ag and microbial researchers jump 
on the microarray bandwagon.

> Gordon
>> Thanks in advance,
>> Jake Michaelson

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