MAplot                 package:affy                 R Documentation

_R_e_l_a_t_i_v_e _M _v_s. _A _p_l_o_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     Create boxplots of M or M vs A plots. Where M is determined
     relative to a specified chip or to a pseudo-median reference chip.

_U_s_a_g_e:

     MAplot(object,...)
     Mbox(object,...)
     ma.plot(A, M, subset = sample(1:length(M), min(c(10000, length(M)))),
     show.statistics=TRUE, span=2/3, family.loess="gaussian", cex = 2,plot.method=c("normal","smoothScatter","add"),add.loess = TRUE,lwd = 1, lty = 1, loess.col = "red",...)

_A_r_g_u_m_e_n_t_s:

  object: An 'AffyBatch-class'

     ...: Additional parameters for the routine

       A: A vector to plot along the horizonal axis

       M: A vector to plot along vertical axis

  subset: A set of indices to use when drawing the loess curve

show.statistics: If true some summary statistics of the M values are
          drawn

    span: span to be used for loess fit.

family.loess: '"guassian"' or '"symmetric"' as in 'loess'.

     cex: Size of text when writing summary statistics on plot

plot.method: a string specifying how the plot is to be drawn.
          '"normal"' plots points, '"smoothScatter"' uses the
          'smoothScatter' function. Specifying '"add"' means that the
          MAplot should be added to the current plot

add.loess: add a loess line to the plot

     lwd: width of loess line

     lty: line type for loess line

loess.col: color for loess line

_S_e_e _A_l_s_o:

     'mva.pairs'

_E_x_a_m_p_l_e_s:

        data(affybatch.example)
        MAplot(affybatch.example)
        Mbox(affybatch.example)