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")
     }

