qualBoxplot           package:arrayQuality           R Documentation

_C_o_m_p_a_r_a_t_i_v_e _b_o_x_p_l_o_t _f_o_r _g_e_n_e_r_a_l _h_y_b_r_i_d_i_z_a_t_i_o_n _Q_u_a_l_i_t_y _C_o_n_t_r_o_l

_D_e_s_c_r_i_p_t_i_o_n:

     This functions allows you to graphically compare your slide
     quality measures to results obtained for a database of 'good
     quality' slides.

_U_s_a_g_e:

     qualBoxplot(arrayQuality = NULL, reference = NULL, organism = c("Mm", "Hs"), DEBUG=FALSE,...)

_A_r_g_u_m_e_n_t_s:

arrayQuality: Matrix of quality results from 'slideQuality' or
          'globalQuality'.

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.

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.

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

     ...: additional arguments

_D_e_t_a_i_l_s:

     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'.

_V_a_l_u_e:

     Returns a score vector containing, for each column in
     "arrayQuality", the number of quality measures below the range of
     "reference". The last element of the score vector is the total
     number of quality measures tested.

_A_u_t_h_o_r(_s):

     Agnes Paquet

_S_e_e _A_l_s_o:

     'globalQuality', 'gpQuality', 'spotQuality', 'agQuality'

_E_x_a_m_p_l_e_s:

     #datadir <- system.file("gprQCData", package="arrayQuality")
     #gprData <- readGPR(fnames="9Mm137.gpr", path=datadir)
     #arrayQuality <- slideQuality(gprData, organism="Mm")
     #qualBoxplot(arrayQuality)

