Dear Yanyan You can use the method described in Section 8.2 (Technical Replication) of the Limma User's Guide. Best wishes Gordon >Message: 9 >Date: Fri, 01 Dec 2006 11:52:37 -0500 >From: Yanyan Li <yli at="" mail.jci.tju.edu=""> >Subject: [BioC] Limma with block and replicate measurement >To: bioconductor at stat.math.ethz.ch >Message-ID: <5.2.0.9.0.20061201115049.0348ae18 at mail.jci.tju.edu> >Content-Type: text/plain; charset="us-ascii"; format=flowed > > >Hi Bioconductors: > > > >I am doing Random Block Design for single-color arrays, consider the >following target frame: > >FileName Exp Trt >1 1 A >2 1 B >3 1 C >4 1 D >5 2 A >6 2 B >7 2 C >8 2 D >9 3 A >10 3 B >11 3 C >12 3 D > >Each mRNA has 3 replicates (same y location and different x location), I am >not a biology person, I hope I could express clearly. > >Now I want to compare pairwise groups across the 3 experiments, treat Exp >as block factor (random) and each mRNA is repeated. > >How to incorporate random and repeated effects to lmFit command and also >contrast. >Is anyone deal with similar situation or any other suggestions? > > >I appreciate all your help. > > > >Thanks a lot > > > >yanyan > > >The documents accompanying this transmission may contain confidential >health or business information. This information is intended for the use >of the individual or entity named above. If you have received this >information in error, please notify the sender immediately and arrange for >the return or destruction of these documents. > >Yanyan Li phone: 215-503-9876, fax: 215-503-3804 >MS. Biostatistician >Division of Biostatistics >Department of Pharmacology and Experimental Therapeutics >Thomas Jefferson University >1015 Chestnut St., Suite M100, Mezzanine Floor >Philadelphia, PA 19107