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(cluster,
           object,
           refindex = 1, FUN = mean, na.rm = TRUE,
           phenoData = new("AnnotatedDataFrame"), cdfname = NULL,
           verbose = FALSE)  
            
     normalizeConstantParaSF1(refindexname)
     normalizeConstantParaSF2(refconstant, refindexname, FUN = mean, na.rm = TRUE)

_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.

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. 

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

refindexname: The name of the array used as reference. 

refconstant: The constant calculated by 'FUN' from the reference array.
          This value will be used for scaling. 

_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.

     'normalizeConstantParaSF1' and 'normalizeConstantParaSF2' are
     internal function which will be executed at all slaves.

'_n_o_r_m_a_l_i_z_e_C_o_n_s_t_a_n_t_P_a_r_a_S_F_1' Calculates and returns intensities from the
     refindex array. 

'_n_o_r_m_a_l_i_z_e_C_o_n_s_t_a_n_t_P_a_r_a_S_F_2' Normalizes the arrays at all slaves. 

_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)

       c1 <- makeCluster(3)

       AffyBatch <- normalizeAffyBatchConstantPara(c1, Dilution, verbose=TRUE)

       stopCluster(c1)
     }
     ## End(Not run)

