preproPara             package:affyPara             R Documentation

_P_a_r_a_l_l_e_l_i_z_e_d _p_r_e_p_r_o_c_e_s_s_i_n_g

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

     Parallelized preprocessing function, which goes from raw probe
     intensities to expression values in three steps: Background
     correction, normalization and summarization

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

     preproPara(cluster,
         object,
         bgcorrect = TRUE, bgcorrect.method = NULL, bgcorrect.param = list(),
         normalize = TRUE, normalize.method = NULL, normalize.param = list(),
         pmcorrect.method = NULL, pmcorrect.param = list(),
         summary.method = NULL, summary.param = list(),
         ids = NULL,phenoData = new("AnnotatedDataFrame"), cdfname = NULL,
         verbose = FALSE)

_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.

bgcorrect: A boolean to express whether background correction is wanted
          or not. 

bgcorrect.method: The name of the background adjustment method to use. 

bgcorrect.param: A list of parameters for 'bgcorrect.method' (if
          needed/wanted) 

normalize: A boolean to express whether normalization is wanted or not. 

normalize.method: The name of the normalization method to use. 

normalize.param: A list of parameters to be passed to the normalization
          method (if wanted). 

pmcorrect.method: The name of the PM adjustement method. 

pmcorrect.param: A list of parameters for 'pmcorrect.method' (if
          needed/wanted). 

summary.method: The method used for the computation of expression
          values 

summary.param: A list of parameters to be passed to the
          'summary.method' (if wanted). 

     ids: List of 'ids' for summarization 

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. 

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

     Parallelized preprocessing function, which goes from raw probe
     intensities to expression values in three steps: Background
     correction, normalization and summarization

     For the serial function and more details see the function
     'expresso'.

     For using this function a computer cluster using the 'snow'
     package has to be started.

     Available methods:

'_b_g_c_o_r_r_e_c_t._m_e_t_h_o_d': see 'bgcorrect.methods'

'_n_o_r_m_a_l_i_z_e._m_e_t_h_o_d': 'quantil', 'constant', 'invariantset'

'_s_u_m_m_a_r_y._m_e_t_h_o_d': see 'generateExprSet.methods'

_V_a_l_u_e:

     An object of class ExpressionSet.

_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)

     esset <- preproPara(cluster,
         affybatch.example,
         bgcorrect = TRUE, bgcorrect.method = "rma2",
         normalize = TRUE, normalize.method = "quantil",
         pmcorrect.method = "pmonly",
         summary.method = "avgdiff",
         verbose = TRUE)
         
     stopCluster(c1)
     ## End(Not run)

