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.

     Sample names that have an underscore in them have it replaced by a
     dot. Underscore causes a number of problems with Latex, if it is
     not escaped.

_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)