backgroundCorrect           package:limma           R Documentation

_C_o_r_r_e_c_t _I_n_t_e_n_s_i_t_i_e_s _f_o_r _B_a_c_k_g_r_o_u_n_d

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

     Background correct microarray expression intensities.

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

     backgroundCorrect(RG, method="subtract", printer=RG$printer)

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

      RG: an 'RGList' object or a unclassed list containing the same
          components as an 'RGList'

  method: character string specifying correction method.  Possible
          values are '"none"', '"subtract"', '"half"', '"minimum"',
          '"movingmin"' or '"edwards"'.

 printer: a list containing printer layout information, see
          'PrintLayout-class'

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

     If 'method="none"' then the corrected intensities are equal to the
     foreground intensities, i.e., the background intensities are
     treated as zero. If 'method="subtract"' then this function simply
     subtracts the background intensities from the foreground
     intensities which is the usual background correction method. If
     'method="half"' then any intensity which is less than 0.5 after
     background subtraction is reset to be equal to 0.5. If
     'method="minimum"' then any intensity which is zero or negative
     after background subtraction is set equal to half the minimum of
     the positive corrected intensities for that array. If
     'method="movingmin"' then the background estimates are replaced
     with the minimums of the backgrounds of the spot and its eight
     neighbors, i.e., the background is replaced by a moving minimum of
     3x3 grids of spots. If 'method="edwards"' a log-linear
     interpolation method is used to adjust lower intensities as in
     Edwards (2003).

     Background correction (background subtraction) is also performed
     by the 'normalizeWithinArrays' method for 'RGList' objects, so it
     is not necessary to call 'backgroundCorrect' directly unless one
     wants to use a method other than simple subtraction. Calling
     'backgroundCorrect' before 'normalizeWithinArrays' will over-ride
     the default background correction.

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

     An 'RGList' object in which components 'R' and 'G' are background
     corrected and components 'Rb' and 'Gb' are removed.

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

     Gordon Smyth

_R_e_f_e_r_e_n_c_e_s:

     Edwards, D. E. (2003). Non-linear normalization and background
     correction in one-channel cDNA microarray studies _Bioinformatics_
     19, 825-833. 

     Yang, Y. H., Buckley, M. J., Dudoit, S., and Speed, T. P. (2002).
     Comparison of methods for image analysis on cDNA microarray data.
     _Journal of Computational and Graphical Statistics_ 11, 108-136.

     Yang, Y. H., Buckley, M. J., and Speed, T. P. (2001). Analysis of
     microarray images. _Briefings in Bioinformatics_ 2, 341-349.

_S_e_e _A_l_s_o:

     An overview of normalization and background correction functions
     is given in '4.Normalization'.

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

     RG <- new("RGList", list(R=c(1,2,3,4),G=c(1,2,3,4),Rb=c(2,2,2,2),Gb=c(2,2,2,2)))
     backgroundCorrect(RG)
     backgroundCorrect(RG, method="half")
     backgroundCorrect(RG, method="minimum")

