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:

     Apply background correction to microarray expression intensities.

_U_s_a_g_e:

     backgroundCorrect(RG, method="subtract")

_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"' or
          '"edwards"'.

_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="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:

     'read.maimages', 'normalizeWithinArrays'

_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")

