backgroundCorrect2           package:OLIN           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:

     Background correction based on 'backgroundCorrect' of the 'limma'
     package.

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

     backgroundCorrect2(object,method="subtract", offset=0)

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

  object: object of class 'marrayRaw'

  method: method for background correction:  none, subtract,
          half, minimum, movingmin, edwards or normexp. 

  offset: 

     {numeric value to add to intensities}

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

     This function is a wrapper function for 'backgroundCorrect' with
     following methods implemented:

        *  none: no background correction

        *  subtract: simple subtraction of background intensities

        *  movingmin: background intensities are first averaged over
           3x3 grids of neighbouring spots and subsequently substracted

        *  minimum: zero or negative intensities after background
           correction are set equal to half the minimum of positive
           corrected intensities

        *  edwards: background correction based on  log-linear
           interpolation 

        *  normexp: background correction based on fitting procedure 

     For further details and references, please refer to its help page.
     An alternative Bayesian model for background correction
     ('kooperberg') is also implemented in the 'limma' package.

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

     Background correct object of class 'marrayRaw'.

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

     Matthias Futschik

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

     'backgroundCorrect','kooperberg'

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

     # Loading data
     data(sw)

     #No background correction
       sw.none <- backgroundCorrect2(sw,method="none")
       plot(maA(sw.none)[,1],maM(sw.none)[,1])

     # Simple subtraction
       sw.sub <- backgroundCorrect2(sw,method="sub")
       points(maA(sw.sub)[,1],maM(sw.sub)[,1],col="red")
      

