bg.correct               package:affy               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 corrects probe intensities in an object of class
     'AffyBatch'.

_U_s_a_g_e:

     bg.correct(object, method, ...)

     bg.correct.rma(object,...)
     bg.correct.mas(object, griddim)
     bg.correct.none(object, ...)

_A_r_g_u_m_e_n_t_s:

  object: An object of class 'AffyBatch'.

  method: A 'character' that defines what background correction method
          will be used. Available methods are given by
          'bg.correct.methods'. 

 griddim: grid dimension used for mas background estimate. The array is
          divided into griddm equal parts. Default is 16.

     ...: arguments to pass along to the engine function.

_D_e_t_a_i_l_s:

     The name of the method to apply must be double-quoted. Methods
     provided with the package are currently:

        *  bg.correct.none: returns 'object' unchanged.

        *  bg.correct.chipwide: noise correction as described in a
           `white paper' from Affymetrix.

        *  bg.correct.rma: the model based correction used by the RMA
           expression measure.

     They are listed in the variable 'bg.correct.methods'. The user
     must supply the word after "bg.correct", i.e none, subtractmm,
     rma, etc...

     More details are available in the vignette.

     R implementations similar in function to the internal
     implemntation used by 'bg.correct.rma' are in 'bg.adjust'.

_V_a_l_u_e:

     An 'AffyBatch' for which the intensities have been background
     adjusted. For some methods (RMA), only PMs are corrected and the
     MMs remain the same.

_E_x_a_m_p_l_e_s:

     if (require(affydata)) {
       data(Dilution)

       ##bgc will be the bg corrected version of Dilution
       bgc <- bg.correct(Dilution, method="rma") 

       ##This plot shows the tranformation
       plot(pm(Dilution)[,1],pm(bgc)[,1],log="xy",
       main="PMs before and after background correction")
     }

