Dear list, I have the following samples: wt-1 mut-1 wt-2 mut-2 wt-3 mut-3 wt-4 mut-4 The wt and the mut come from different plants. Question is, which is a better design?? To pool all the wt and used that as a common reference or use a loop design as follows. cy3 cy5 wt-1 mut-1 mut-1 wt-2 wt-2 mut-2 mut-2 wt-3 wt-3 mut-3 mut-3 wt-4 wt-4 mut-4 mut-4 wt-1 In addition, which Bioconductor package can be used the analysis of the loop design? Thank you for any suggestions. Sohail Khan Scientific Programmer COLD SPRING HARBOR LABORATORY Genome Research Center 500 Sunnyside Boulevard Woodbury, NY 11797 (516)422-4076

The best design depends on which comparisons are of most interest to you. If you have 2 genotypes (wt and mutant) with 4 replicates of each and your objective is to compare wt to mutant, you are probably fine with a dye-swap design with 4 arrays, 1 wt and 1 mut on each array. If the mutants are all different genotypes, then you need to replicate the mutants. (In my opinion, this should be a separate set of plants - or at least a separate RNA extraction). The best design depends on which comparisons are of most interest - comparisons among the mutants, or comparisons of each mutant to wt. I cannot think of a situation in which I would want to use the loop design you have indicated below. The main principle to remember is that the comparisons with most power are the 2 samples on the same array. --Naomi At 05:01 PM 1/10/2006, Khan, Sohail wrote: >Dear list, > >I have the following samples: > >wt-1 mut-1 >wt-2 mut-2 >wt-3 mut-3 >wt-4 mut-4 > >The wt and the mut come from different plants. Question is, which is >a better design?? >To pool all the wt and used that as a common reference or use a loop >design as follows. >cy3 cy5 >wt-1 mut-1 >mut-1 wt-2 >wt-2 mut-2 >mut-2 wt-3 >wt-3 mut-3 >mut-3 wt-4 >wt-4 mut-4 >mut-4 wt-1 >In addition, which Bioconductor package can be used the analysis of >the loop design? Thank you for any suggestions. > > > > >Sohail Khan >Scientific Programmer >COLD SPRING HARBOR LABORATORY >Genome Research Center >500 Sunnyside Boulevard >Woodbury, NY 11797 >(516)422-4076 > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111