computeExprSetPara         package:affyPara         R Documentation

_P_a_r_a_l_l_e_l _g_e_n_e_r_a_t_e _a _s_e_t _o_f _e_x_p_r_e_s_s_i_o_n _v_a_l_u_e_s

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

     Parallel generation of a set of expression values from the probe
     pair information. The set of expression is returned as an
     ExpressionSet object.

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

     computeExprSetPara(cluster,
         object,
         ids = NULL,
         pmcorrect.method, summary.method,
         summary.param = list(), pmcorrect.param = list(),
         phenoData = new("AnnotatedDataFrame"), cdfname = NULL,
         verbose = 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.

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 one steps: summarization

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

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

_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)
     if (require(affydata)) {
       data(Dilution)

       c1 <- makeCluster(3)

       esset <- computeExprSetPara(cluster,
           Dilution,
           pmcorrect.method = "pmonly",
           summary.method = "avgdiff",
           verbose = TRUE)

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

