hi....... Richard Friedman <friedman at="" ...=""> writes: > > Dear Bioconductor Users, > I am trying to use LimmaGUI to analyze a CpG island experiment. > > I wish to calculate the statistical significance associated with the > comparison > (Tumor Undigested-Tumor Digested) vs. (Normal Undigested-Normal > digested). > (Undigested has both methylated and unmethylated CpG islands. Digested > has only > Unmethylated CpG islands. So Undigested-Digested gives the extent of > methylation. > > Comparing tumor to normal gives the change in methylation associated > with cancer. > > > > Mytarget matrix is: > SlideNumber FileName Cy3 Cy5 Date > > 18370n_13430283.spot Ndigest Nundigest 10/3/06 > 28370n_13430572.spot Nundigest Ndigest 10/3/06 > 38370t_13469544.spot Tdigest Tundigest10/17/06 > 48370t_13469546.spot TundigestTdigest 10/17/06 > > <snip> You are trying to estimate an interaction (ie, 'difference of differences'). The message explains why it is not possible to do this with the present design: the design is unconnected. The present design looks like: ND ---> NU ND <--- NU TD ---> TU TD <--- TU so there is no path connecting any N with any T. To estimate the interaction you will also need hybs like Nx ---> Ty (and/or vice versa), where x and y are D and/or U. Then you can use limma/limmaGUI to estimate the difference you are interested in. Best regards, Darlene -- Darlene Goldstein ?cole Polytechnique F?d?rale de Lausanne (EPFL) Institut de math?matiques B?timent MA, Station 8 Tel: +41 21 693 5565 CH-1015 Lausanne Fax: +41 21 693 4303 SWITZERLAND