Wenbin, I have found this link quite useful for figuring out design matrix for direct designs: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? cmd=Retrieve&db=PubMed&list_uids=14744830&dopt=Abstract Sean On May 31, 2005, at 11:32 AM, Wenbin Liu wrote: > Thanks, Gordon! In the expanded example, you have a > common RNA source, the Pool. What if one doesn't have > a common RNA source, such as when it is a loop design > with more than three arrays like the unexpanded Weaver > data? Can you please show me how to generate the > matrices? Thanks! > > > Wenbin > > --- Gordon K Smyth <smyth@wehi.edu.au> wrote: > >> I guess that you are using an older version of the >> software. The Weaver example was expanded and >> simplified last October, and full commands are now >> given to compute the design matrix, including >> use of modelMatrix() and makeContrasts(). >> >> Gordon >> >> ------ original message -------- >> [BioC] limma example Weaver Data >> Wenbin Liu wnbnl at yahoo.com >> Thu May 26 23:25:09 CEST 2005 >> >> Dear Gordon and limma users, >> >> I'm struggling to understand the design matrices in >> the Weaver Data in the Case Studies section of the >> limma User's Guide. >> >> In the single loop design, there are 4 arrays and 4 >> conditions (from two time points and two genotypes). >> I tried using modelMatrix() with the target from the >> example and assigning ref='P11WT'. I would like to >> check the effect 'TimeWt' which is the late vs. >> early >> for WT. Unfortunately, I have been unable to get >> Gordon's result (topTable result). >> >> Can someone show me how to get Gordon's design >> matrices (two of them in that example) by using the >> function modelMatrix() and probably plus >> makeContrasts()? >> >> Thanks in advance! >> >> Sincerely, >> Wenbin >> >> >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor