normalizeAffyBatchInvariantsetPara package:affyPara R Documentation

_P_a_r_a_l_l_e_l_i_z_e_d _I_n_v_a_r_i_a_n_t_e _S_e_t _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 using an invariant set.

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

     normalizeAffyBatchInvariantsetPara(object,
         prd.td = c(0.003, 0.007), baseline.type = c("mean", "median", "pseudo-mean", "pseudo-median"),
         type = c("separate", "pmonly", "mmonly", "together"),
         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.

  prd.td: A cutoff parameter for normalization. 

baseline.type: Specify how to determine the baseline array (mean,
          median). 

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

phenoData: A 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 normalization of arrays using an invariant set. The
     set of invariant intensities between data and ref is found through
     an iterative process (based on the respective ranks the
     intensities). This set of intensities is used to generate a
     normalization curve by smoothing.

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

     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 <- normalizeAffyBatchInvariantsetPara(Dilution, verbose=TRUE)

       stopCluster()
     }
     ## End(Not run)

