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