Hi : 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]]

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]]