Hi When ignoring duplicate spots, the functions "readTargets", "modelMatrix" and "makeContrasts" helps to construct the design matrix. Are there similar functions for "automatic" generation of the design vector when considering duplicate spots using "duplicateCorrelation" and "gls.series"? Looking forward hearing from you! Jakob ------------------------------------------------------ Jakob Hedegaard Danish Institute of Agricultural Sciences Department of Animal Breeding and Genetics Research Centre Foulum P.O. Box 50 DK-8830 Tjele, Denmark Tel: (+45) 8999 1363 Fax: (+45) 8999 1300

On Wed, 23 Jun 2004, Jakob Hedegaard wrote: > When ignoring duplicate spots, the functions "readTargets", > "modelMatrix" and "makeContrasts" helps to construct the > design matrix. > Are there similar functions for "automatic" generation of the > design vector when considering duplicate spots using > "duplicateCorrelation" and "gls.series"? Jakob, In limma, the within-array duplicate spots are handled in a very different way from the replicate arrays, so while the design matrix depends on the replicate array structure, it doesn't depend on the within-array duplicate spot structure, so you can just use the same functions: readTargets, modelMatrix etc. Instead of using a design matrix to tell limma about your duplicate spot structure, you use the ndups and spacing arguments of the duplicateCorrelation function. Hope this help, James