normalizeAffyBatchQuantilesPara   package:affyPara   R Documentation

_P_a_r_a_l_l_e_l_i_z_e_d _q_u_a_n_t_i_l_e _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 normalization of arrays based upon quantiles.

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

     normalizeAffyBatchQuantilesPara(object,
         phenoData = new("AnnotatedDataFrame"), cdfname = NULL,
         type = c("separate", "pmonly", "mmonly", "together"), 
         cluster, verbose = getOption("verbose"))

     normalizeQuantilesPara(cluster, type, object.length, 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. 

 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. 

    type: A string specifying how the normalization should be applied.

 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") 

object.length: Number of samples, which should be normalized. 

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

     Parallelized normalization of arrays based upon quantiles.  This
     method is based upon the concept of a quantile-quantile plot
     extended to 'n' dimensions.  No special allowances are made for
     outliers.

     For the serial function and more details see the function
     'normalize.AffyBatch.quantiles'.

     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.

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

     '_n_o_r_m_a_l_i_z_e_Q_u_a_n_t_i_l_e_s_P_a_r_a' Function for quantile normalization.

_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 <- normalizeAffyBatchQuantilesPara(Dilution, verbose=TRUE)

       stopCluster()
     }
     ## End(Not run)

