I generally find it easier to do a single channel analysis for these more complicated designs. Just follow the manual for single channel and you can then use the treatments directly to form the contrasts. --Naomi At 12:14 PM 10/31/2008, Adrian Johnson wrote: >Hi : >sorry for re-sending the my question. Lookinf forward for some help. thanks. >I searched bioconductor list archive and could not find appropriate >modelmatrix and contrast matrix fitting >for the following type of data from two color. > > > > targets > Array Cy3 Cy5 Treatment Shock >1 Array1 WT MU Y H >2 Array2 WT MU N C >3 Array3 WT MU Y H >4 Array4 MU WT N C >5 Array5 WT MU Y C >6 Array6 WT MU Y C > > >I want to compare (MU.WT-Y) - (MU.WT-N) >and (MU.WT-H)-(MU.WT-C) > >How can I design my model matrix and fit contrasts. > >Could some one help me please. > >thanks >Ad. > > [[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 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