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.

        'bg.correct.rma2' gives access to the older background method
        that was used by the 'rma' function in version 1.1 bioconductor
        releases. For the 1.2 release 'rma' performs the same
        background adjustment as 'bg.correct.rma'. Unless you wish to
        duplicate older results in which case you should use
        'bg.correct.rma'.

        Details on the internal fucntions 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")