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: \begin{itemize}

     *  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. \end{itemize}

        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:

         data(affybatch.example)

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

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

