plotMA               package:codelink               R Documentation

_M_A _p_l_o_t

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

     Takes a Codelink object and plot M vs A.

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

       plotMA(object, array1=1, array2=2, cutoff=NULL, label="type", type=NULL,
             high.list=NULL, high.col="blue", high.pch="*",
             snr.cutoff=1, legend.x="bottomright", pch=".", subset=NULL, 
             title=NULL, xlim=NULL, ylim=NULL)

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

  object: an object of class "Codelink" or "MAarrayLM".

  array1: first array to be used.

  array2: second array to be used.

  cutoff: cutoff to be used as fold change markeer.

   label: type of labeling used in legend.

    type: spot type information.

high.list: list of genes highlighted.

high.col: color used for high genes.

high.pch: pch used for high genes.

snr.cutoff: SNR cutoff used for label spots.

legend.x: relative position of the legend.

     pch: pch style used to main spots.

  subset: subset of spots used to plot based on 'type' slot.

   title: title of the plot.

    xlim: range for the X axis.

    ylim: range for the Y axis.

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

     The plot is for M=(array2-array1) vs A=(array2+array1)/2.

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

_N_o_t_e:

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

     Diego Dez Ruiz

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

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

     #    data(codelink.example)
     #    plotMA(codelink.example)

