BufferedMatrix.justRMA package:BufferedMatrixMethods R Documentation

_U_s_e _B_u_f_f_e_r_e_d_M_a_t_r_i_x _o_b_j_e_c_t_s _t_o _f_a_c_i_l_i_t_a_t_e _R_M_A _c_o_m_p_u_t_a_t_i_o_n _w_i_t_h _l_o_w _m_e_m_o_r_y _o_v_e_r_h_e_a_d

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

     Read CEL data into 'BufferedMatrix' objects.

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

     BufferedMatrix.justRMA(..., filenames=character(0),celfile.path=NULL,
                          phenoData=new("AnnotatedDataFrame"),
                          description=NULL,
                          notes="",
                          verbose=FALSE, background=TRUE, normalize=TRUE,
                          cdfname = NULL)

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

     ...: file names separated by comma.

filenames: file names in a character vector.

celfile.path: path where CEL files are located

phenoData: a 'AnnotatedDataFrame' object

description: a 'MIAME' object 

   notes: notes 

 verbose: verbosity flag 

normalize: logical value. If 'TRUE' normalize data using quantile
          normalization

background: logical value. If 'TRUE' background correct using RMA
          background correction

 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.

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

     An 'ExpressionSet' object, containing expression values identical
     to what one would get from running 'rma' on an 'AffyBatch'.

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

     Ben Bolstad bmb@bmbolstad.com

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

     'BufferedMatrix', 'BufferedMatrix.read.probematrix'

