plotSA                 package:limma                 R Documentation

_S_i_g_m_a _v_s _A _p_l_o_t _f_o_r _m_i_c_r_o_a_r_r_a_y _l_i_n_e_a_r _m_o_d_e_l

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

     Plot log residual standard deviation versus average log expression
     for a fitted microarray linear model.

_U_s_a_g_e:

     plotSA(fit, xlab="Average log-expression", ylab="log2(sigma)", zero.weights=FALSE, pch=16, cex=0.2, ...)

_A_r_g_u_m_e_n_t_s:

     fit: an 'MArrayLM' object.

    xlab: character string giving label for x-axis

    ylab: character string giving label for y-axis

     pch: vector or list of plotting characters. Default is integer
          code 16 which gives a solid circle.

     cex: numeric expansion factor for plotting character.  Defaults to
          0.2.

zero.weights: logical, should spots with zero or negative weights be
          plotted?

     ...: any other arguments are passed to 'plot'

_D_e_t_a_i_l_s:

     This plot is used to check the mean-variance relationship of the
     expression data, after fitting a linear model.

     See 'points' for possible values for 'pch' and 'cex'.

_V_a_l_u_e:

     A plot is created on the current graphics device.

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

     Gordon Smyth

_S_e_e _A_l_s_o:

     An overview of diagnostic functions available in LIMMA is given in
     09.Diagnostics.

