qualityDiagnostics        package:arrayMagic        R Documentation

_G_e_n_e_r_a_t_e_s _q_u_a_l_i_t_y _d_i_a_g_n_o_s_t_i_c _p_l_o_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     Several quality diagnostic plots are generated. The distributions
     of the (normalised) intensities, as well as overall similarities
     between hybridisations and several other quality parameters are
     graphically visualised (cf. function 'qualityParameters').

_U_s_a_g_e:

     qualityDiagnostics(arrayDataObject, exprSetRGObject, qualityParametersList, groupingColumn, slideNameColumn, savePath=".", completeOutput=FALSE, verbose=TRUE, plotOutput="pdf")

_A_r_g_u_m_e_n_t_s:

arrayDataObject: 'arrayData-class'; required; default: missing

exprSetRGObject: 'exprSetRG-class'; required, default: missing

qualityParametersList: the return value of 'qualityParameters'
          required; default: missing

groupingColumn: character string; optional; default: missing; specifies
          a column of 'pDataSlide(exprSetRGObject)' which is used to
          indicate the hybridisation groups in the clustered similarity
          plots.

slideNameColumn: character string; optional; default: missing;
          specifies a column of 'pDataSlide(exprSetRGObject)'.

savePath: character string; required; default: "."

completeOutput: required; default: 'FALSE'

 verbose: logical; required; default: 'TRUE'

plotOutput: character string specifying the output type; either
          "screen", "pdf" or "win.metafile"; default: "pdf"

_D_e_t_a_i_l_s:

_V_a_l_u_e:

     The function is called for its side effect.

_A_u_t_h_o_r(_s):

     Andreas Buness <a.buness@dkfz.de>

_S_e_e _A_l_s_o:

     'qualityParameters', 'exprSetRG-class', 'arrayData-class'

_E_x_a_m_p_l_e_s:

             

