core                  package:daMA                  R Documentation

_I_n_t_e_r_n_a_l _f_u_n_c_t_i_o_n _o_f _a_n_a_l_y_s_e_M_A

_D_e_s_c_r_i_p_t_i_o_n:

     This internal function of analyseMA computes the statistics and
     estimators that are organised and given out by the main function
     analyseMA.

_U_s_a_g_e:

     core(vector, design, cmat, cinfo, tol)

_A_r_g_u_m_e_n_t_s:

  vector: a simple help variable for the apply call

  design: the design matrix of size N times (K+2), where K is the
          number of experimental conditions. This is the design matrix
          X known from linear model theory and its elements are
          typically 0, 1, or -1. A 0 means that the associated
          parameter does not apply for the corresponding observation
          (i.e., row). The first two columns are reserved for the two
          dyes and are usually filled up with 1 and -1, respectively. 

    cmat: a matrix describing the p experimental questions (contrasts)
          to be analysed in the experiment. The matrix can be composed
          of vectorial contrasts (a single row of the matrix) and of
          contrasts in matrix form (several rows of the matrix), e.g.
          an A times B interaction effect in a 3 times 2 design. All
          contrasts have to be combined into one matrix (using rbind
          for instance). 

   cinfo: a vector of length p describing the grouping of the contrast
          matrix rows in vector or matrix  form. E.g. if the design
          matrix contains three contrasts in vector form, cinfo =
          rep(1,3), if it contains two vectorial contratst and one as
          matrix with three rows, cinfo=c(1,1,3). 

     tol: A value indicating the tolerance for contrast estimability
          check 

_A_u_t_h_o_r(_s):

     Jobst Landgrebe (jlandgr1@gwdg.de) and Frank Bretz
     (bretz@bioinf.uni-hannover.de)

_R_e_f_e_r_e_n_c_e_s:

     Bretz, F and Landgrebe J and Brunner E (2003):"Design and analysis
     of two colour factorial microarray experiments", submitted. <URL:
     http://www.microarrays.med.uni-goettingen.de/>

