Hi all I'm working on data from an Agilent array that has the following design: Cy3 ~ Cy5 Treated(SampleA) ~ Control(SampleA) Control(SampleA) ~ Treated(SampleA) Treated(SampleB) ~ Control(SampleC) Control(SampleD) ~ Treated(SampleE) i.e. the first dye swap pair is with the same sample, the second is with four different samples. What is the correct way to specify the design? Thanks in advance!

Dear Anonymous, you could try with reading the "Two color" chapter of the "Bioconductor Case Studies" book (Hahne et al., 2008). Best wishes Wolfgang aculeata at gmail.com scripsit 01/14/2010 08:03 PM: > Hi all > > I'm working on data from an Agilent array that has the following design: > > Cy3 ~ Cy5 > Treated(SampleA) ~ Control(SampleA) > Control(SampleA) ~ Treated(SampleA) > Treated(SampleB) ~ Control(SampleC) > Control(SampleD) ~ Treated(SampleE) > > i.e. the first dye swap pair is with the same sample, the second is > with four different samples. What is the correct way to specify the > design? > > Thanks in advance! > > _______________________________________________ > 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 -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber/contact