bkgdCorrect             package:codelink             R Documentation

_B_a_c_k_g_r_o_u_n_d _c_o_r_r_e_c_t_i_o_n _o_f _i_n_t_e_n_s_i_t_y _v_a_l_u_e_s.

_D_e_s_c_r_i_p_t_i_o_n:

     Takes a Codelink object with Spot mean and Bkgd median values and
     corrects applying one of the methods available.

_U_s_a_g_e:

       bkgdCorrect(object, method = "half", preserve = FALSE, verbose = FALSE,
         offset = 0)

_A_r_g_u_m_e_n_t_s:

  object: character; an object of class "Codelink".

  method: character; the correction method to use, one of "none",
          "subtract", "half" and "normexp".

preserve: logical; if Smean and Bmedian slots should be preserved.

 verbose: logical; if TRUE print some information with method normexp.

  offset: numeric; value to add to intensities.

_D_e_t_a_i_l_s:

     Available methods are: . none: left intensities untouched. .
     subtract: simple subtraction of Bkgd median from Spot mean. .
     half: the same as above but aboid negative values setting all
     intensity values below zero to 0.5. . normexp: apply normexp
     background adjustment from package limma.

_V_a_l_u_e:

     An object of class Codelink with corrected intensity values, that
     is Ri slot.

_A_u_t_h_o_r(_s):

     Diego Diez

_E_x_a_m_p_l_e_s:

     ## Not run: 
         data(codelink.example)
         codelink.example <- bkgdCorrect(codelink.example, method = "half")
     ## End(Not run)

