combineAffyBatch         package:matchprobes         R Documentation

_A _f_u_n_c_t_i_o_n _t_o _c_o_m_b_i_n_e _d_a_t_a _f_r_o_m _d_i_f_f_e_r_e_n_t _A_f_f_y_m_e_t_r_i_x _g_e_n_e_c_h_i_p _t_y_p_e_s
_i_n_t_o _o_n_e _A_f_f_y_B_a_t_c_h.

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

     The function takes a list of AffyBatches and their respective
     probe sequence information and merges the intensities from the
     matching probes only into one AffyBatch.

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

     combineAffyBatch(batch, probepkg, newcdf, verbose=TRUE)

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

   batch: A 'list' of AffyBatches.

probepkg: A character vector of the same length as 'batch', containing
          the names of the probe sequences libraries (for example,
          'hgu133aprobe') that go with the AffyBatches.

  newcdf: Character. The name of the name CDF environment that is to be
          created.

 verbose: Logical. If TRUE, messages are printed to the console.

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

     Note that batch effects may play an important role, e.g. because
     of slightly but systematically different reagents or sample
     treatments in the experiments at led to the data in the different
     AffyBatches. Thus, please interprete the results of this function
     with caution.

     Probe to probe-set mapping: after the common probes between all
     AffyBatches have been identified, their mapping into probe sets
     (=the new CDF environment) is obtained from the restriction of the
     mapping of the first element of 'batch' (see variable 'REFCHIP' in
     the code).

     If you want to use this function, please have a look at its code
     and if necessary, check intermediate results.

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

     A list with two elements: 'dat', an 'AffyBatch', and 'cdf', an
     environment that contains the probe-set to probe mapping.

     The phenoData slot of 'dat' will be empty. This is because in most
     cases this requires some manual interference. You will need to
     construct a combined phenoData slot by yourself.

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

     R. Gentleman, Wolfgang Huber

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

       ## see vignette!

