normalizeAffyBatchConstantPara   package:affyPara   R Documentation

_P_a_r_a_l_l_e_l_i_z_e_d _s_c_a_l_i_n_g _n_o_r_m_a_l_i_z_a_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     Parallelized scaling normalization of arrays.

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

     normalizeAffyBatchConstantPara(object,
           refindex = 1, FUN = mean, na.rm = TRUE,
           phenoData = new("AnnotatedDataFrame"), cdfname = NULL,
           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.

refindex: The index of the array used as reference. 

     FUN: A function generating a value from the intensities on an
          array.  Typically 'mean' or 'median'. 

   na.rm: Paramater passed to the function FUN. A logical value
          indicating whether 'NA' values  should be stripped before the
          computation proceeds. 

phenoData: An AnnotatedDataFrame object. 

 cdfname: Used to specify the name of an alternative cdf package. If
          set to 'NULL',  the usual cdf package based on Affymetrix'
          mappings will be used. 

 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.
          default: getOption("verbose") 

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

     Parallelized scaling normalization of arrays. This means that all
     the array are scaled so that they have the same mean value.

     For the serial function and more details see the function
     'normalize.constant'.

     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 of normalized objects.

_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)

       AffyBatch <- normalizeAffyBatchConstantPara(Dilution, verbose=TRUE)

       stopCluster()
     }
     ## End(Not run)

