updateDesign            package:designGG            R Documentation

_U_p_d_a_t_e_s _c_u_r_r_e_n_t _d_e_s_i_g_n

_D_e_s_c_r_i_p_t_i_o_n:

     Updates current experimental design (including 'array.allocation'
     and 'condition.allocation').

_U_s_a_g_e:

       updateDesign( array.allocation, condition.allocation, nRILs, 
                     nSlides, nEnvFactors, nTuple, btwoColorArray )

_A_r_g_u_m_e_n_t_s:

array.allocation: matrix with nArray rows and nRIL columns. Elements of
          1/0 indicate this RIL (or strain) is/not selected  for this
          array.  

condition.allocation: matrix with nCondition rows and nRIL columns.
          Elements of 1/0 indicate this RIL (or strain) is/not selected
           for this condition.   

   nRILs: number of RILs (or strains) available for the experiment.  

 nSlides: total number of slides available for experiment.  

nEnvFactors: number of environmental factors, an integer bewteen 1 and
          3. When 'nEnvFactors' is 1 and the number of levels for the
          enviromental factor  ('nLevels')is 1, there is one condition
          in the experiment (i.e. no  enviromental perturbation) and
          thus only genetic factor will be considered in the algorithm.
          When 'nEnvFactors' is 1 and nLevels is larger than 1 or
          'nEnvFactors' is larger than 1, all main factor(s) and
          interacting facotr(s) will be included. Examples: If there is
          a temperature perturbation, then 'nEnvFactors' is 1; If there
          is both temperature and drug treatment perturbation,  then
          'nEnvFactors' is 2. 

  nTuple: average number of RILs (or strains) to be assigned onto each
          condition. 
           'nTuple' should be a real number which is larger than 1.
           If 'nTuple' < 1, the algorithm will stop and show the
          message, 
           'warning: "The number of slides is too small to perform the
          experiment."' 

bTwoColorArray: binary variable indicating experiment type: 
           'bTwoColorArray <- T' #for dual channel experiment 
           'bTwoColorArray <- F' #for single channel experiment  

_D_e_t_a_i_l_s:

     This function calls two subfunctions: 'conditionUpdate' and
     'arrayUpdate'.

_V_a_l_u_e:

     a list with two elements, 'array.allocation' and
     'condition.allocation'.

_A_u_t_h_o_r(_s):

     Yang Li <yang.li@rug.nl>, Gonzalo Vera
     <gonzalo.vera.rodriguez@gmail.com> 
      Rainer Breitling <r.breitling@rug.nl>, Ritsert Jansen
     <r.c.jansen@rug.nl>

_R_e_f_e_r_e_n_c_e_s:

     Y. Li, R. Breitling and R.C. Jansen. Generalizing genetical
     genomics: the added value from environmental perturbation, Trends
     Genet (2008) 24:518-524. 
      Y. Li, M. Swertz, G. Vera, J. Fu, R. Breitling, and R.C. Jansen.
     designGG: An R-package and Web tool for the optimal design of
     genetical genomics experiments. (submitted) 
      http://gbic.biol.rug.nl/designGG

