anova.MAList-method          package:limma          R Documentation

_A_N_O_V_A _T_a_b_l_e - _m_e_t_h_o_d

_D_e_s_c_r_i_p_t_i_o_n:

     Analysis of variance method for objects of class 'MAList'.
     Produces an ANOVA table useful for quality assessment by
     decomposing between and within gene sums of squares for a series
     of replicate arrays. This method produces a single ANOVA Table
     rather than one for each gene and is not used to identify
     differentially expressed genes.

_U_s_a_g_e:

     'anova(object,design=NULL,ndups=2,...)'

_A_r_g_u_m_e_n_t_s:

     '_o_b_j_e_c_t' object of class 'MAList'. Missing values in the M-values
          are not allowed.

     '_d_e_s_i_g_n' numeric matrix containing the design matrix for linear
          model. The number of rows should agree with the number of
          columns of M. The number of columns will determine the number
          of coefficients estimated for each gene.

     '_n_d_u_p_s' number of duplicate spots. Each gene is printed ndups
          times in adjacent spots on each array.

     '...' other arguments are not used

_D_e_t_a_i_l_s:

     This function aids in quality assessment of microarray data and in
     the comparison of normalization methodologies.

_V_a_l_u_e:

     An object of class 'anova' containing rows for between genes,
     between arrays, gene x array interaction, and between duplicate
     with array sums of squares. Variance components are estimated for
     each source of variation.

_A_u_t_h_o_r(_s):

     Gordon Smyth

_S_e_e _A_l_s_o:

     'MAList-class', 'bwss.matrix', 'anova'.

     An overview of quality assessment and diagnostic functions in
     LIMMA is given by 6.Diagnostics.

