Dear List, I am working on yeast data that has 11 positive controls replicated 17 times. They are irregularly located in the array. After obtaining MA object, I could order the genes and get them next to each other. My question is, how would I incorporate the duplicate correlation aspect when defining the design in limma? Thank you for your reply and help. Yolande [[alternative HTML version deleted]]

Hi Yolande, duplicateCorrelation is designed for the situations where all spots are printed 2 or more times, not for handling a small number of probes that have been spotted many times. This is what the help page refers to as "regularly spaced within-array replicate spots" cheers, Mark ----------------------------------------------------- Mark Cowley, BSc (Bioinformatics)(Hons) Peter Wills Bioinformatics Centre Garvan Institute of Medical Research, Sydney, Australia ----------------------------------------------------- On 05/08/2008, at 3:29 AM, Yolande Tra wrote: > Dear List, > > I am working on yeast data that has 11 positive controls replicated > 17 times. They are irregularly located in the array. After obtaining > MA object, I could order the genes and get them next to each other. > My question is, how would I incorporate the duplicate correlation > aspect when defining the design in limma? > Thank you for your reply and help. > > Yolande > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor