09.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_F_B'  Plots foreground versus background log-intensies for a
          two-color array.

      '_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. 'mdplot' can also be useful for comparing two
          one-channel microarrays.

      '_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.

      '_p_l_o_t_M_D_S'  Multidimensional scaling plot for a set of arrays.
          Useful for visualizing the relationship between the set of
          samples.

      '_p_l_o_t_S_A'  Sigma vs A plot. After a linear model is fitted, this
          checks constancy of the variance with respect to intensity
          level.

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

_A_u_t_h_o_r(_s):

     Gordon Smyth