affycomp.figures.auxiliary     package:affycomp     R Documentation

_A_u_x_i_l_i_a_r_y _f_u_n_c_t_i_o_n_s _t_o _c_r_e_a_t_e _F_i_g_u_r_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     These functions are auxiliary function to 'affycompPlot'. These
     Figures are used to assess an expression measure. They take
     components created by the 'assessDilution' and 'assessSpikeIn'
     functions.

_U_s_a_g_e:

     affycomp.figure1(l,main="Figure 1",xlim=NULL,ylim=NULL)
     affycomp.figure1b(l,main="Figure 1b",xlim=NULL,ylim=NULL,cex=0.85,all=FALSE)
     affycomp.figure2(l,main="Figure 2")
     affycomp.figure2b(l,main="Figure 2b")
     affycomp.figure3(l, main = "Figure 3")
     affycomp.figure4a(l, main = "Figure 4a",equal.lims=FALSE)
     affycomp.figure4b(l, main = "Figure 4b")
     affycomp.figure4c(l, rotate=TRUE, main = "Figure 4c")
     affycomp.figure5a(l, main = "Figure 5a",maxfp=100)
     affycomp.figure5b(l, main = "Figure 5b",maxfp=100)
     affycomp.figure5c(l, main = "Figure 5c",maxfp=100)
     affycomp.figure5d(l, main = "Figure 5d",maxfp=100)
     affycomp.figure5e(l, main = "Figure 5e",maxfp=100)
     affycomp.figure6a(l, main = "Figure 6a",xlim = NULL, ylim = NULL)
     affycomp.figure6b(l, main = "Figure 6b",xlim = NULL, ylim = NULL)

_A_r_g_u_m_e_n_t_s:

       l: A list with the necessary components to create the Figure.
          See details.

    main: Title for the Figure.

   maxfp: range of the false positives in ROC will be from 0 to 'maxfp'

    xlim: x-axis limits.

    ylim: y-axis limits.

     cex: size of numbers in figure 1b.

     all: logical. If 'TRUE' all spikeins are shown. Otherwise, only
          those resulting in smaller, realistic, fold changes are
          shown.

equal.lims: logical. If 'TRUE' the limits of x-axis and y-axis will
          have same range.

  rotate: in the case of compfig4c one can eiher show the actual local
          slopes or the bias (local slope minus 1).

_D_e_t_a_i_l_s:

     Read the vignette for more details on what each Figure is. You can
     read 'assessSpikeIn' and 'assessDilution' to see which assessments
     are needed.

_V_a_l_u_e:

     Figures are produced.

_A_u_t_h_o_r(_s):

     Rafael A. Irizarry

_E_x_a_m_p_l_e_s:

     data(rma.assessment)
     affycomp.figure1(rma.assessment$MA)
     affycomp.figure2(rma.assessment$Dilution)
     affycomp.figure3(rma.assessment$Dilution)
     affycomp.figure4a(rma.assessment$Signal)
     affycomp.figure4b(rma.assessment$Dilution)
     affycomp.figure5a(rma.assessment$FC)
     affycomp.figure5b(rma.assessment$FC2)
     affycomp.figure6a(rma.assessment$FC)
     affycomp.figure6b(rma.assessment$FC)

