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

     normalizeQuantilesPara(cluster, type, object.length, verbose=FALSE)
     normalizeQuantilesParaSF1(type)
     normalizeQuantilesParaSF2(row_mean)

_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. 

 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.

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

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

row_mean: Row mean used for normalization. 

_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.

     'normalizeQuantilesPara', 'normalizeQuantilesParaSF1' and
     'normalizeQuantilesParaSF2' are 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 quantil normalization.

'_n_o_r_m_a_l_i_z_e_Q_u_a_n_t_i_l_e_s_P_a_r_a_S_F_1' Slavefuntion to calculate row means.

'_n_o_r_m_a_l_i_z_e_Q_u_a_n_t_i_l_e_s_P_a_r_a_S_F_2' Slavefunction to do 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)

     data(affybatch.example)

     c1 <- makeCluster(3)

     AffyBatch <- normalizeAffyBatchQuantilesPara(c1, affybatch.example, verbose=TRUE)

     stopCluster(c1)
     ## End(Not run)

