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

