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

[Steve Lianoglou]

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