targets          package:Agi4x44PreProcess          R Documentation

_E_x_a_m_p_l_e _o_f _t_a_r_g_e_t _f_i_l_e

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

     Example of target file

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

     data(targets)

_F_o_r_m_a_t:

     A data frame with 4 observations on the following 5 variables.

     '_F_i_l_e_N_a_m_e' names of the Files 'Ast.txt' 'Bst.txt' 'Aunst.txt'
          'Bunst.txt'

     '_T_r_e_a_t_m_e_n_t' Assigns level for Treatment Effect to each File
          (mandatory)

     '_G_E_r_e_p' a numeric vector tha numerates the FACTOR of the Treatment
          Effect (mandatory)

     '_S_u_b_j_e_c_t' Assigns level for Subject Effect to each file (optional)

     '_A_r_r_a_y' Assigns level for Array Effect to each file  (optional)

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

     It is a tab-delimited text format file.  The target file is
     created with the intention of carrying out a differential
     expression analysis   in future steps using 'limma'. Therefore,
     here is where  factors that are going to be included in the 
     linear model that is fitted to each gen are specified.  Targets
     file assigns each image data file to one  of the experimental
     conditions of the experiment.  First column 'FileName' is
     mandatory and includes image data files names. Second column
     'Treatment' is also mandatory and includes treament effect. Third
     column 'GErep' is also mandatory, and includes the Treatment
     effect in a numeric code, from  1 to n, being n the number of
     Treatment effect levels. The rest of the columns are optional, and
     they  can include other factors that we want to specify in  the
     model, such as 'Subject', 'Array', and so on.

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

     Gordon K. Smyth, M. Ritchie, N. Thorne, J. Wettenhall (2007).
     limma: Linear Models for Microarray Data User's Guide.

_E_x_a_m_p_l_e_s:

     ## Not run: 
             data(targets)
     ## End(Not run)

