swaps or always controls with same dye?
In many experiments we have to decide whether to use dye-swap (i.e., each treatment gets Cy3 and Cy5, in different slides, of course) or to always have the control with one dye (e.g., Cy3) and the experimentals with the other. Some papers on experimental design for arrays deal with these issues. Two excelent papers, very well written and easy to read are: • Yang and Speed’s 2002 Nature Review Genetics paper. • Churchill’s 2002 Nature Genetics paper. Slightly more technical are: • Kerr’s 2003 tech. report. 210. • Speed and Yang’s 2002 Sankhya paper. • Dobbin et al.’s 2003 paper. And from the Bioconductor list: • Rossini.
