Dear list: There is a data set, consisting of 3 Agilent slides. The experiment was run with direct hybridization, knock-out versus wild-type, and no dye swap. Due to difficulty of collecting samples, the samples were pooled and hybridized onto 3 separate slides. Of course the 3 slides are not biological replicates. They are not pure technical replicates either. How should I set up a design matrix for limma model analysis? Thanks! JP- ################################## Jianping Jin Ph.D. Bioinformatics scientist Center for Bioinformatics Room 3133 Bioinformatics building CB# 7104 University of Chapel Hill Chapel Hill, NC 27599 Phone: (919)843-6105 FAX: (919)843-3103 E-Mail: jjin at email.unc.edu

On 7/31/06 2:49 PM, "Jianping Jin" <jjin at="" email.unc.edu=""> wrote: > > Dear list: > > There is a data set, consisting of 3 Agilent slides. The experiment was run > with direct hybridization, knock-out versus wild-type, and no dye swap. Due > to difficulty of collecting samples, the samples were pooled and hybridized > onto 3 separate slides. How were the samples pooled? Were they pooled and then split, or are there three distinct biologic replicates? The lack of dye swap IS a problem, as you will likely find dye-biased probes (potentially MANY). > Of course the 3 slides are not biological replicates. They are not pure > technical replicates either. How should I set up a design matrix for limma > model analysis? You'll need to be a bit more specific about how you did the pooling.... Sean