magetab2bioc          package:ArrayExpress          R Documentation

_C_o_n_v_e_r_t _M_A_G_E-_T_A_B _f_i_l_e_s _f_r_o_m _r_a_w _d_a_t_a _i_n_t_o _a _B_i_o_c_o_n_d_u_c_t_o_r _o_b_j_e_c_t

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

     'magetab2bioc' converts local MAGE-TAB files into a AffyBatch, an
     ExpressionSet or a NChannelSet.

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

     magetab2bioc(files, rawcol = NULL)

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

   files: A list as given from 'getAE' function. Containing the
          following elements:

          _r_a_w_f_i_l_e_s all the expression files to use to create the
               object. The content of the raw.zip MAGE-TAB file.

          _s_d_r_f the name of the sdrf file from MAGE-TAB.

          _i_d_f the name of the idf file from MAGE-TAB.

          _a_d_f the name of the adf file from MAGE-TAB.

          _p_a_t_h is the name of the directory containing these files.

  rawcol: by default, the columns are automatically selected according
          to the scanner type. If the scanner is unknown or if the user
          wants to use different columns than the default, the argument
          'rawcol' can be set. For two colour arrays it must be a list
          with the fields 'R', 'G', 'Rb' and 'Gb' giving the column
          names to be used for red and green foreground and background.
          For one colour arrays, it must be a character string with the
          column name to be used. These column names must correspond to
          existing column names of the expression files.

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

     An object of class 'AffyBatch', 'ExpressionSet' or  'NChannelSet'
     with the raw expression values in the 'assayData' of the object,
     the information contained in the sdrf file in the 'phenoData', the
     adf file content in the 'featureData' and the idf file content in
     the 'experimentData'.

     If several array designs are used in the dataset, the output is a
     list with an object for each array design.

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

     Audrey Kauffmann  Maintainer: <audrey@ebi.ac.uk>

_S_e_e _A_l_s_o:

     'queryAE', 'getAE'

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

     # An example can be found in the help of the getAE function.
      

