pumaFull                package:puma                R Documentation

_P_e_r_f_o_r_m _a _f_u_l_l _P_U_M_A _a_n_a_l_y_s_i_s

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

     Full analysis including pumaPCA and mmgmos/pumaDE vs rma/limma
     comparison

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

     pumaFull (
             affybatch = NULL
     ,       data_dir = getwd()
     ,       load_affybatch = FALSE
     ,       calculate_eset = TRUE
     ,       calculate_pumaPCAs = TRUE
     ,       calculate_bcomb = TRUE
     ,       mmgmosComparisons = FALSE
     )

_A_r_g_u_m_e_n_t_s:

affybatch: An object of class 'AffyBatch'. 

data_dir: A character string specifying where data files are stored. 

load_affybatch: Boolean. Load a pre-existing AffyBatch object? Note
          that this has to be named "affybatch.rda" and be in the
          'data_dir' directory. 

calculate_eset: Boolean. Calculate ExpressionSet from 'affybatch'
          object? If FALSE, files named "eset_mmgmos.rda" and
          "eset_rma.rda" must be available in the 'data_dir' directory. 

calculate_pumaPCAs: Boolean. Calculate pumaPCA from 'eset_mmgmos'
          object? If FALSE, a file named "pumaPCA_results.rda" must be
          available in the 'data_dir' directory. 

calculate_bcomb: Boolean. Calculate pumaComb from 'eset_mmgmos' object?
          If FALSE, files named "eset_comb.rda" and
          "eset_normd_comb.rda" must be available in the 'data_dir'
          directory. 

mmgmosComparisons: Boolean. If TRUE, will compare mmgmos with default
          settings, with mmgmos used with background correction. 

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

     No return values. Various objects are saved as .rda files during
     the execution of this function, and various PDF files are created.

_A_u_t_h_o_r(_s):

     Richard D. Pearson

_S_e_e _A_l_s_o:

     Related methods 'pumaDE', 'createDesignMatrix' and
     'createContrastMatrix'

_E_x_a_m_p_l_e_s:

             data(affybatch.example)
             pData(affybatch.example) <- data.frame("level"=c("twenty","twenty","ten")
                 , "batch"=c("A","B","A"), row.names=rownames(pData(affybatch.example)))
             pumaFull(affybatch.example)

