pairs.AffyBatch             package:affy             R Documentation

_p_l_o_t _i_n_t_e_n_s_i_t_i_e_s _u_s_i_n_g '_p_a_i_r_s'

_D_e_s_c_r_i_p_t_i_o_n:

     Plot intensities using the function 'pairs'

_U_s_a_g_e:

     ## S3 method for class 'AffyBatch':
     pairs(x, panel=points, ..., transfo=I, main=NULL, oma=NULL,
                       font.main = par("font.main"),
                       cex.main = par("cex.main"), cex.labels = NULL, 
                       lower.panel=panel, upper.panel=NULL, diag.panel=NULL,
                       font.labels = 1, row1attop = TRUE, gap = 1)

_A_r_g_u_m_e_n_t_s:

       x: an 'AffyBatch' object 

   panel: a function to produce a plot (see 'pairs') 

     ...: extra parameters for the 'panel' function

 transfo: a function to transform the intensity values before
          generating the plot. 'log' and 'log2' are popular choices. 

    main: title for the plot

     oma: see 'oma' in 'par'.

font.main: see 'pairs'

cex.main: see 'pairs'

cex.labels: see 'pairs'

lower.panel: a function to produce the plots in the lower triangle (see
          'pairs').

upper.panel: a function to produce the plots in the upper triangle (see
          'pairs').

diag.panel: a function to produce the plots in the diagonal (see
          'pairs').

font.labels: see 'pairs'

row1attop: see 'pairs'

     gap: see 'pairs'

_D_e_t_a_i_l_s:

     Plots with several chips can represent zillions of points. They
     require a lot of memory and can be very slow to be displayed. You
     may want to try to split of the plots, or to plot them in a device
     like 'png' or 'jpeg'.

