affycompPlot            package:affycomp            R Documentation

_A_s_s_e_s_s_m_e_n_t _P_l_o_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     Function that makes assessment plot

_U_s_a_g_e:

     affycompPlot(...,assessment.list=NULL,method.names=NULL,
                  figure1.xlim=c(-4,15),figure1.ylim=c(-10,12),
                  figure1b.xlim=c(-4,15),figure1b.ylim=c(-6,5),
                  figure6a.xlim=c(-12,12),figure6a.ylim=c(-12,12),
                  figure6b.xlim=c(-3,3),figure6b.ylim=c(-6,6))

     affycomp.compfigs(l,method.names=NULL,
                       figure1.xlim=c(-4,15),figure1.ylim=c(-10,12),
                       figure1b.xlim=figure1b.xlim,figure1b.ylim=figure1b.ylim,
                       figure6a.xlim=c(-12,12),figure6a.ylim=c(-12,12),
                       figure6b.xlim=c(-3,3),figure6b.ylim=c(-6,6))
     affycomp.figures(l)
     affycomp.figure.calls(what)
     affycomp.compfigs.calls(what)

_A_r_g_u_m_e_n_t_s:

     ...: lists produced by the assessment functions (one for each
          method) separated by commas.

assessment.list: Alternatively, one can also send a list of lists
          produced by one of the assessment functions

method.names: A character vector with the names of the epxression
          measure methodology.

figure1.xlim: x-axis lim used for the plots in Figure 1.

figure1.ylim: y-axis lim used for the plots in Figure 1.

figure1b.xlim: x-axis lim used for the plots in Figure 1b.

figure1b.ylim: y-axis lim used for the plots in Figure 1b.

figure6a.xlim: x-axis lim used for the plots in Figure 6a.

figure6a.ylim: y-axis lim used for the plots in Figure 6a.

figure6b.xlim: x-axis lim used for the plots in Figure 6b.

figure6b.ylim: y-axis lim used for the plots in Figure 6b.

       l: list with assessment lists as components.

    what: a dummy variable to know what function call to create.

_D_e_t_a_i_l_s:

     Read the vignette for more details on what each Figure is. Once an
     assessment is used this function knows what to do. You can call
     any of the assessment functions described in 'assessSpikeIn',
     'assessDilution' and 'assessSD'.

     'affycomp.figures', 'affycomp.figure.calls',
     'affycomp.compfigs.calls' are auxiliary functions.

_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)
     affycompPlot(rma.assessment,mas5.assessment)
     affycompPlot(rma.assessment$FC)
     affycompPlot(rma.assessment$Dilution,mas5.assessment$Dilution)
     affycompPlot(rma.assessment$Dilution,mas5.assessment$Dilution)
     affycompPlot(rma.assessment$Signal,mas5.assessment$Signal)
     affycompPlot(rma.assessment$Dilution,mas5.assessment$Dilution)
     affycompPlot(rma.assessment$FC2,mas5.assessment$FC2)

