spotQuality           package:arrayQuality           R Documentation

_D_i_a_g_n_o_s_t_i_c _p_l_o_t_s _a_n_d _c_o_m_p_a_r_a_t_i_v_e _b_o_x_p_l_o_t_s _f_o_r _g_e_n_e_r_a_l
_h_y_b_r_i_d_i_z_a_t_i_o_n, _S_p_o_t _f_o_r_m_a_t

_D_e_s_c_r_i_p_t_i_o_n:

     This component provides qualitative diagnostic plots and
     quantitative measures for assessing general hybridization quality.
     All results are displayed in a HTML report. Spot format only.

_U_s_a_g_e:

     spotQuality(fnames = NULL, path = ".", galfile = NULL, organism = c("Mm", "Hs"),
     compBoxplot = TRUE, reference = NULL, controlMatrix = controlCode,
     controlId = c("ID"), output = FALSE, resdir = ".", dev= "png", DEBUG = FALSE,...)

_A_r_g_u_m_e_n_t_s:

  fnames: A "character" string naming the input files.

    path: A "character" string representing the data directory.  By
          default this is set to the current working directory (".").

 galfile: A "character" string naming the galfile associated with the
          input files. If galfile = NULL, spotQuality will use the
          first .gal file available in the working directory.

organism: A "character" string naming the organism genome printed on
          the array, either "Mm" or "Hs". By default, organism is set
          to "Mm". It is used to retrieve the corresponding reference
          tables.

compBoxplot: Logical. If set to 'FALSE', only qualitative diagnostic
          plots will be plotted. gpQuality ouput will be limited to a
          diagnostic plot by gpr file and a marrayRaw object.

reference: A matrix resulting from globalQuality, to be used as
          reference table to compare slides. If 'NULL', the default
          table corresponding to organism will be used. See details for
          more information.

controlMatrix: A character matrix of n by 2 columns. The first column
          contains a few regular expression of spotted probe sequences
          and the second column contains the corresponding control
          status.

controlId: Character string. Name of the column of the gpr file used to
          define controls.

  output: Logical. If 'TRUE', normalized M values corresponding to the
          input GenePix files and quality measures are printed to a
          file.

  resdir: A "character" string representing the directory where the
          results will be saved. By default, this is set to the current
          working directory ("."). 

     dev: A "character" string naming the graphics device. This will
          take arguments "png", "jpeg" and "ps" only. By default, dev
          is set to "png".

   DEBUG: If 'TRUE', debug statements are printed.

     ...: additional arguments

_D_e_t_a_i_l_s:

     agQuality returns 2 plots for each Agilent files passed as
     argument. The first one is a qualitative diagnostic plot, a quick
     visual way to assess slide quality. The second one is a
     comparative boxplot: each quality control measure is compared to
     the range obtained for a database of 'good' slides used as
     reference. You can use your own set of references created using
     'globalQuality' passed in the arguments "reference", or use the
     reference QC values stored in the datasets 'MmReferenceDB' and
     'HsReferenceDB'. All results and quality scores are gathered in a
     HTML report. For more details about the QC measures and the plots,
     please refer to the online manual.

_V_a_l_u_e:

     A list of 2 elements:

    mraw: A marrayRaw object created from the input files.

 quality: A matrix containing Quality Control measures for all slides.

_A_u_t_h_o_r(_s):

     Agnes Paquet

_S_e_e _A_l_s_o:

     'globalQuality', 'qualBoxplot', 'readAgilent'

_E_x_a_m_p_l_e_s:

