spkMA                package:spkTools                R Documentation

_M_A _P_l_o_t_s

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

     Plots log-ratios (M) vs. average log expression (A) for a
     SpikeInExpressionSet object.

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

     spkMA(object, spkSlopeOut, fc=2, tol=3, label=NULL, ylim=NULL,
     outlier=1, reduce=TRUE, plot.legend=TRUE)

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

  object: a SpikeInExpressionSet object

spkSlopeOut: the output from the spkSlope function

      fc: the fold change of interest

     tol: the precision (number of digits after decimal point) in fc

   label: a character string to insert into the plot title

    ylim: limits of y-axis

 outlier: log fold change cut-off for outliers

  reduce: if TRUE some points are removed from the background to speed
          plotting

plot.legend: if TRUE a legend is plotted

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

     The MA plot is produced.

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

     Matthew N. McCall

_E_x_a_m_p_l_e_s:

     data(affy)
     affySlope <- spkSlope(affy)
     spkMA(affy, affySlope)

