ArrayExpress          package:ArrayExpress          R Documentation

_R _o_b_j_e_c_t_s _f_r_o_m _A_r_r_a_y_E_x_p_r_e_s_s _d_a_t_a_b_a_s_e

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

     'ArrayExpress' produces an AffyBatch, an ExpressionSet or an
     NChannelSet from a raw data set from the ArrayExpress database.
     'ArrayExpress' needs an Internet connection.

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

     ArrayExpress(input, path = ".", save = TRUE, rawcol = NULL)

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

   input: an ArrayExpress identifier. The package currently covers 96%
          of the raw data sets of the database and is not currently
          dealing with the processed data.

    path: the name of the directory in which the files downloaded on
          the ArrayExpress repository will be extracted. The default is
          the current directory.

    save: if TRUE, the files downloaded from the database will not be
          deleted from path after executing the function.

  rawcol: by default, for the raw data, 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:

     The output is an object of class 'AffyBatch' or  '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 in the featureData, and the idf file
     content in the experimentData.

     If several array designs are used in the data set, 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', 'magetab2bioc'

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

     ETABM25.affybatch = ArrayExpress(input = "E-TABM-25")
     print(ETABM25.affybatch)
     sampleNames(ETABM25.affybatch)
     colnames(pData(ETABM25.affybatch))

