qc.read.file           package:simpleaffy           R Documentation

_R_e_a_d _a _f_i_l_e _d_e_f_i_n_i_n_g _t_h_e _Q_C _p_a_r_a_m_e_t_e_r_s _f_o_r _a _s_p_e_c_i_f_i_e_d _a_r_r_a_y _a_n_d
_s_e_t _u_p _t_h_e _Q_C _E_n_v_i_r_o_n_m_e_n_t

_D_e_s_c_r_i_p_t_i_o_n:

     Affymetrix define a series of QC parameters for their arrays. Many
     of these rely on specific probeset that differ between arrays and
     are used to calculate things like 3'/5' ratios. See 'qc.affy' for
     more details. This is usually done by a call to
     'setQCEnvironment'; the function described here is the one that
     does the actual loading of the configuration file.  See the
     package vignette for details of the config file's syntax.

_U_s_a_g_e:

       qc.read.file(fn)

_A_r_g_u_m_e_n_t_s:

      fn: full path and name of the file to load 

_V_a_l_u_e:

     none.

_N_o_t_e:

_A_u_t_h_o_r(_s):

     Crispin J Miller

_R_e_f_e_r_e_n_c_e_s:

     http://bioinformatics.picr.man.ac.uk/

_S_e_e _A_l_s_o:

     'setQCEnvironment'

_E_x_a_m_p_l_e_s:

       fn <- system.file("extdata","hgu133plus2cdf.qcdef",package="simpleaffy")
       qc.read.file(fn)
       qc.get.spikes()
       qc.get.probes()
       qc.get.ratios()