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'.

     'backgroundCorrect' uses utility functions 'ma3x3.matrix',
     'ma3x3.spottedarray', 'normexp.fit', 'normexp.signal' and
     'normexp.m2loglik', 'normexp.grad'.

     '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 columns of the
     GenePix data files which are not read in by 'read.maimages', so
     you will need to use 'read.series' instead of 'read.maimages' if
     you wish to use 'kooperberg'.

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

     Gordon Smyth

