affycomp.compfigs.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 _c_o_m_p_a_r_i_t_i_v_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 compare expression measures. They take lists
     with components created by the 'assessDilution' and
     'assessSpikeIn' functions.

_U_s_a_g_e:

     affycomp.compfig2(l, method.names = as.character(1:length(l)),
                       add.legend = TRUE, main = "Figure 2")

     affycomp.compfig3(l, method.names = as.character(1:length(l)),
                       main = "Figure 3")

     affycomp.compfig4a(l, method.names = as.character(1:length(l)),
                        add.legend = TRUE, main = "Figure 4a")

     affycomp.compfig4b(l, method.names = as.character(1:length(l)),
                        add.legend = TRUE, main = "Figure 4b")

     affycomp.compfig4c(l, method.names = as.character(1:length(l)),
                        add.legend = TRUE, rotate=TRUE, main = "Figure 4c")

     affycomp.compfig5a(l, method.names = as.character(1:length(l)),
                       add.legend = TRUE, main = "Figure 5a", maxfp=100)

     affycomp.compfig5b(l, method.names = as.character(1:length(l)),
                       add.legend = TRUE, main = "Figure 5b", maxfp=100)

     affycomp.compfig5cdef(l, method.names = as.character(1:length(l)),
                       add.legend = TRUE, main = "Figure 5c", maxfp=100,
                       type=c("low","medlow","medhigh","high")

     affycomp.compfig5c(l, method.names = as.character(1:length(l)),
                       add.legend = TRUE, main = "Figure 5c", maxfp=100)

     affycomp.compfig5d(l, method.names = as.character(1:length(l)),
                       add.legend = TRUE, main = "Figure 5d", maxfp=100)

     affycomp.compfig5e(l, method.names = as.character(1:length(l)),
                       add.legend = TRUE, main = "Figure 5e", maxfp=100)

     affycomp.compfig5f(l, method.names = as.character(1:length(l)),
                       add.legend = TRUE, main = "Figure 5f", maxfp=100)

_A_r_g_u_m_e_n_t_s:

       l: a list of lists with the necessary components to create the
          Figure. See details.

method.names: a character vector with the names of the expression
          measures methodologies being compared. 

add.legend: logical. If TRUE a legend is added.

    main: title of the Figure.

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

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

    type: compfig5cdef is the engine for 5c, 5d, 5e, and 5f. 'type'
          tells is which of these 4 to run.

_D_e_t_a_i_l_s:

     These are similar to the functions defined in
     'affycomp.figures.auxiliary'. Main difference is that here you
     send lists with the result of the assessment functions as
     components.

_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)
     data(mas5.assessment)
     affycomp.compfig2(list(rma.assessment$Dilution,mas5.assessment$Dilution))
     affycomp.compfig3(list(rma.assessment$Dilution,mas5.assessment$Dilution))
     affycomp.compfig4a(list(rma.assessment$Signal,mas5.assessment$Signal))
     affycomp.compfig4b(list(rma.assessment$Dilution,mas5.assessment$Dilution))
     affycomp.compfig5a(list(rma.assessment$FC,mas5.assessment$FC))
     affycomp.compfig5b(list(rma.assessment$FC2,mas5.assessment$FC2))

