setQCEnvironment         package:simpleaffy         R Documentation

_E_s_t_a_b_l_i_s_h _t_h_e _a_p_p_r_o_p_r_i_a_t_e _Q_C _e_n_v_i_r_o_n_m_e_n_t _f_o_r _t_h_e _s_p_e_c_i_f_i_e_d _a_r_r_a_y

_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. These functions are used to set up the appropriate
     QC environment for the specified array. This is done by loading a
     configuration file, either from the packages data directory, or
     from the specified path. See the package vignette for details of
     the config file's syntax.

_U_s_a_g_e:

      setQCEnvironment(array,path=NULL)

_A_r_g_u_m_e_n_t_s:

   array: This should be the 'clean' cdf name of the array as generated
          by 'cleancdfname' in the affy package.

    path: Path to the file. By default, checks the package's own data
          directory - only needed if a defininition file is being
          specified manually, as described in the vignette.

_D_e_t_a_i_l_s:

     The usual way to get the 'clean' cdfname is as follows:
     'cleancdfname(cdfName(eset))', where 'eset' is an 'AffyBatch'
     object.

_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:

     'qc'

_E_x_a_m_p_l_e_s:

       setQCEnvironment("hgu133plus2cdf")
       setQCEnvironment(cleancdfname("HG-U133_Plus_2"))