affyQAReport          package:affyQCReport          R Documentation

_G_e_n_e_r_a_t_e _a _Q_A _R_e_p_o_r_t _f_o_r _A_f_f_y_m_e_t_r_i_x _a_r_r_a_y_s

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

     These functions provide a method for creating, viewing and
     removing QA reports on an experiment run on Affymetrix CEL files.

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

     affyQAReport(affyB, output = "pdf", outdir = file.path(getwd(), "affyQA"), 
            overwrite = FALSE, repName)
     rmQAReport(x)
     openQAReport(x)

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

   affyB: An instance of the 'AffyBatch' class. 

  output: Type of output wanted, currently only pdf is supported. 

  outdir: The directory (or folder) where output will be directed.

overwrite: Whether an existing report, with the same name, should be
          overwritten.

 repName: A character string indicating the name of the report. 

       x: A character string containing the location of the directory 
          holding the report.

_D_e_t_a_i_l_s:

     A wide variety of tools from different packages are used, in
     conjunction  with Sweave tools to produce an integrated document
     with various statistics that should help determine whether there
     are data quality problems with the data.

     This package only works for Affymetrix data. It requires a working
     LaTeX implementation and so is not likely to work on Windows
     platforms, and in some cases on OS X unless the user has installed
     these tools.

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

     A list with the following components is returned. 

 qcStats: The QC statistics computed by the 'simpleaffy' package.

 affyPLM: The QC statistics computed by the 'affyPLM' package.

    MADS: The computed MAD statistic on the 'M' values from an M-A
          decomposition.

     loc: The location (directory/folder) containing the report.

    name: The name of the report.

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

     R. Gentleman

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

     ## Not run: 
        library("affydata")
        data("Dilution")
        affyQAReport(Dilution)
     ## End(Not run)

