read.probematrix            package:affy            R Documentation

_R_e_a_d _C_E_L _f_i_l_e _d_a_t_a _i_n_t_o _P_M _o_r _M_M _m_a_t_r_i_c_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Read CEL data into matrices.

_U_s_a_g_e:

     read.probematrix(..., filenames = character(0),
                    phenoData = new("AnnotatedDataFrame"),
                    description = NULL,
                    notes = "",
                    compress = getOption("BioC")$affy$compress.cel,
                    rm.mask = FALSE, rm.outliers = FALSE, rm.extra = FALSE,
                    verbose = FALSE,which="pm", cdfname = NULL)

_A_r_g_u_m_e_n_t_s:

     ...: file names separated by comma.

filenames: file names in a character vector.

phenoData: a 'AnnotatedDataFrame' object

description: a 'MIAME' object 

   notes: notes 

compress: are the CEL files compressed ?

 rm.mask: should the spots marked as 'MASKS' set to 'NA' ? 

rm.outliers: should the spots marked as 'OUTLIERS' set to 'NA' 

rm.extra: if 'TRUE', overrides what is in 'rm.mask' and 'rm.oultiers' 

 verbose: verbosity flag 

   which: should be either "pm", "mm" or "both"

 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:

     A list of one or two matrices. Each matrix is either PM or MM
     data. No 'AffyBatch' is created.

_A_u_t_h_o_r(_s):

     Ben Bolstad bmb@bmbolstad.com

_S_e_e _A_l_s_o:

     'AffyBatch', 'read.affybatch'

