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 vector or single-column matrix containing the
          design matrix for linear model. The length of the vector or
          the number of rows of the matrix should agree with the number
          of columns of M.

     '_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. It applies only to
     replicated two-color experiments in which all the arrays are
     hybridized with the same RNA targets, possibly with dye-swaps, so
     the design matrix should have only one column. The function has
     not been heavily used and is somewhat experimental.

_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.

_N_o_t_e:

     This function does not give valid results in the presence of
     missing M-values.

_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 09.Diagnostics.