7.Diagnostics             package:limma             R Documentation

_D_i_a_g_n_o_s_t_i_c_s _a_n_d _Q_u_a_l_i_t_y _A_s_s_e_s_s_m_e_n_t

_D_e_s_c_r_i_p_t_i_o_n:

     This page gives an overview of the LIMMA functions available for
     microarray quality assessment and diagnostic plots.

     This package provides an 'anova' method which is designed for
     assessing the quality of an array series or of a normalization
     method. It is not designed to assess differential expression of
     individual genes. 'anova' uses utility functions 'bwss' and
     'bwss.matrix'.

     The function 'arrayWeights' estimates the empirical reliability of
     each array following a linear model fit.

     Diagnostic plots can be produced by


      '_i_m_a_g_e_p_l_o_t'  Produces a spatial picture of any spot-specific
          measure from an array image. If the log-ratios are plotted,
          then this produces an in-silico representation of the well
          known false-color TIFF image of an array. 'imageplot3by2'
          will write imageplots to files, six plots to a page.

      '_p_l_o_t_M_A'  MA-plots. One of the most useful plots of a two-color
          array. 'plotMA3by2' will write MA-plots to files, six plots
          to a page.

      '_p_l_o_t_P_r_i_n_t_T_i_p_L_o_e_s_s'  Produces a grid of MA-plots, one for each
          print-tip group on an array, together with the corresponding
          lowess curve. Intended to help visualize print-tip loess
          normalization.

      '_p_l_o_t_P_r_i_n_t_o_r_d_e_r'  For an array, produces a scatter plot of
          log-ratios or log-intensities by print order.

      '_p_l_o_t_D_e_n_s_i_t_i_e_s'  Individual channel densities for one or more
          arrays. An essential plot to accompany between array
          normalization, especially quantile normalization.

     'plotPrintTipLoess' uses utility functions 'gridr' and 'gridc'.
     'plotDensities' uses utility function 'RG.MA'.

_A_u_t_h_o_r(_s):

     Gordon Smyth

