backgroundNormalise        package:beadarray        R Documentation

_B_a_c_k_g_r_o_u_n_d _N_o_r_m_a_l_i_s_a_t_i_o_n _f_o_r _B_e_a_d _S_u_m_m_a_r_y _D_a_t_a _o_b_j_e_c_t_s

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

     Normalise expression matrix using values of negative controls

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

     backgroundNormalise(object)

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

  object: An ExpressionSetIllumina object

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

     This function implements the background normalisation method
     recommened by Illumina. All normalisation options in BeadStudio
     (with the exception of no normalisation) include background
     normalisation as a first step.

     The QC object contains averaged values for the Illumina negative
     controls placed on each array in an experiment. For background
     normalisation, we simply subtract the value of the negative
     control on a particular array from all bead summary values on that
     array.

     Note that this background normalisation is in addition to a local
     background correction performed at the bead level and is liable to
     create negative values for genes with low expression. It is
     therefore not advisable if you wish to analyse data on a log2
     scale.

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

     Expression matrix containing normalise values with the same
     dimensions as the input

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

     Mark Dunning

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

     #data(BSData)

     #BSData.bgnorm = backgroundNormalise(BSData)

