bgCorrectPara            package:affyPara            R Documentation

_P_a_r_a_l_l_e_l_i_z_e_d _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:

     Parallelized functions for background correction of probe
     intensities.

_U_s_a_g_e:

     bgCorrectPara(object,
             phenoData = new("AnnotatedDataFrame"), method,
             cluster, verbose = getOption("verbose"))

_A_r_g_u_m_e_n_t_s:

  object: An object of class AffyBatch OR  a 'character' vector with
          the names of CEL files  OR a (partitioned) list of
          'character' vectors with CEL file names.

phenoData: An AnnotatedDataFrame object 

  method: A 'character' that defines what background correction method
          will be used.  Available methods are given by
          'bg.correct.methods'.  The name of the method to apply must
          be double-quoted. 

 cluster: A cluster object obtained from the function makeCluster in
          the SNOW package.  For default '.affyParaInternalEnv$cl' 
          will be used. 

 verbose: A logical value. If 'TRUE' it writes out some messages. 

_D_e_t_a_i_l_s:

     'bgCorrectPara' is the parallelized function for background
     correction of probe intensities.  For serial function an more
     details see bg.correct.

     For using this function a computer cluster using the SNOW package
     has to be started.  Starting the cluster with the command
     'makeCluster' generates an cluster object in the affyPara
     environment (.affyParaInternalEnv) and  no cluster object in the
     global environment. The cluster object in the affyPara environment
     will be used as default cluster object,  therefore no more cluster
     object handling is required.   The 'makeXXXcluster' functions from
     the package SNOW can be used to create an cluster object in the
     global environment and  to use it for the preprocessing functions.

_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.

_A_u_t_h_o_r(_s):

     Markus Schmidberger schmidb@ibe.med.uni-muenchen.de, Ulrich
     Mansmann mansmann@ibe.med.uni-muenchen.de

_E_x_a_m_p_l_e_s:

     ## Not run: 
     library(affyPara)
     if (require(affydata)) {
       data(Dilution)

       makeCluster(3)

       ##bgc will be the bg corrected version of Dilution 
       bgc <- bgCorrectPara(Dilution, method="rma", verbose=TRUE)

       stopCluster()
     }
     ## End(Not run)

