The simplest way to handle this is probably to take the difference of the pairs and feed that into limma as a 1-sample t. --Naomi At 12:22 PM 4/20/2004 +1000, Gordon Smyth wrote: >At 03:09 AM 20/04/2004, Danielle Fletcher wrote: >>Hi, >> >>I am using limma to analyse a 2-colour microarray experiment. There are 2 >>treatments and 4 replicates in each of these groups. Each replicate is >>paired to a replicate in the otehr treatment group. Each sample was >>hybridised with a reference, so 8 slides in total. >> >>The targets file looks like this (hopefuly that will make it clearer): >>SlideNumber Name FileName Cy3 Cy5 >>1 1M 1.gpr monolayer ref >>2 1P 5b.gpr pellet ref >>3 2M 2.gpr monolayer ref >>4 2P 7.gpr pellet ref >>5 3M 3.gpr monolayer ref >>6 3P 6.gpr pellet ref >>7 4M B.gpr monolayer ref >>8 4P A.gpr pellet ref >> >>Initially my design matrix looked like this: >> >> Sample-Ref Monolayer-Pellet >>1M 1 0 >>1P 1 1 >>2M 1 0 >>2P 1 1 >>3M 1 0 >>3P 1 1 >>4M 1 0 >>4P 1 1 >> >>but thinking about it again, i don't think this takes into account the >>paired nature of the data. I am sure that the answer is probably a simple one, > >There is no simple answer. There was a big discussion about this in >Bioconductor very recently, please look at the list archives. > >In the very latest versions of limma, there is a new argument 'block' in >duplicateCorrelation() and lmFit() to handle a blocking structure like you >describe. This feature is however very lightly documented so far and so is >offered on a user beware basis. In your case, block=c(1,1,2,2,3,3,4,4). > >Gordon > >> but I am not sure what the best solution is. I would appreciate any >> advice. >> >>Thanks in advance >> >>Danielle > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Bioinformatics Consulting Center Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111