[BioC] LIMMA: data with technical replicate/familial relationship/biological replicate

[Naomi Altman]

If you want to take the family correlation structure into account, 
limma is not the appropriate software.  MAANOVA can handle balanced 
random effects type data - this would use a random effect that 
induces equal correlation among all family members regardless of 
degree of relatedness.  To handle unbalanced family data or familial 
effects determined by the degree of relatedness, you need the more 
flexible correlation structure afforded by software such as 
lme.  However, this does not give you the added power afforded by 
(empirical) Bayesian shrinkage.  As well, you would need to fit gene 
by gene, which will definitely mean very slow run time.

--Naomi


At 02:19 PM 5/13/2010, Steve Lianoglou wrote:
>Hi Qin,
>
>On Thu, May 13, 2010 at 11:38 AM, qin kuang <kuang_qin at hotmail.com> wrote:
> > Thanks Steve.
> >
> > Actually I have done this family by family. I also tried method like GEE to
> > take familial relationship by averaging technical replicates. At 
> this point,
> > looks the methods like LIMMA/GEE can not  two-level/type of 
> dependence (like
> > technical replicate and familial relationship) but only one-level/type of
> > dependence.
> >
> > The reason that I want to look all families together is that some
> > individuals in these families share the same deletion region
> > (this is mRNA expression data, the deletion region was detected in other
> > genomic study). In my previous post, I used 'affected' vs 'unaffected'.
> > Precisely, it is 'deleted' vs 'undeleted'.
> >
> > In your point 2, what do you mean "combine families as biological 
> replicates
> > and do cases vs. controls"? This is what I want to do. As I 
> mentioned above,
> > I can only consider one type of dependence, but the data has two types of
> > dependence.
>
>If that's the case, the limma user's guide goes into a good amount of
>detail about being careful with replicate data: biological and
>technical replicates, and how to rig up your code to incorporate both.
>
>See section 8.2, for instance.
>
>Is this what you're after?
>
>--
>Steve Lianoglou
>Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
>Contact Info: http://cbio.mskcc.org/~lianos/contact
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
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