04.Background             package:limma             R Documentation

_B_a_c_k_g_r_o_u_n_d _C_o_r_r_e_c_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     This page deals with background correction methods for two-color
     microarray data.

     Usually one doesn't need to explicitly ask for background
     correction of the intensities because this is done by default by
     'normalizeWithinArrays', which subtracts the background from the
     foreground intensities before applying the normalization method.
     This default background correction method can be over-ridden by
     using 'backgroundCorrect' which offers a number of alternative
     background correct methods to simple subtraction. The function
     'backgroundCorrect' is used to correct the 'RGList' before
     applying 'normalizeWithinArrays'.

     The 'movingmin' method of 'backgroundCorrect' uses utility
     functions 'ma3x3.matrix' and 'ma3x3.spottedarray'.

     The 'normexp' method of 'backgroundCorrect' uses utility functions
     'normexp.fit' and 'normexp.signal'.

     'kooperberg' is a Bayesian background correction tool designed
     specifically for GenePix data. 'kooperberg' is not currently used
     as the default method for GenePix data because it is
     computationally intensive. It requires several additional columns
     from the GenePix data files which can be read in using
     'read.maimages' and specifying the 'other.columns' argument.

_A_u_t_h_o_r(_s):

     Gordon Smyth

