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

     bgCorrectParaSF(method) 

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

 cluster: A cluster object obtained from the function makeCluster in
          the 'SNOW' package. 

  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. 

 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.

     'bgCorrectParaSF' is a internal function which will be executed at
     slaves.

'_b_g_C_o_r_r_e_c_t_P_a_r_a_S_F' Calls 'bg.correct' at slaves.

_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)

     data(affybatch.example)

     c1 <- makeCluster(3)

     ##bgc will be the bg corrected version of affybatch.example 
     bgc <- bgCorrectPara(c1, affybatch.example, method="rma", verbose=TRUE)

     stopCluster(c1)
     ## End(Not run)

