spkSlope              package:spkTools              R Documentation

_S_i_g_n_a_l _D_e_t_e_c_t _S_l_o_p_e _P_l_o_t

_D_e_s_c_r_i_p_t_i_o_n:

     Plots observed expression vs. nominal concentration. The overall
     regression slope, as well as, regression slopes for low, medium,
     and high bins are computed and the regression lines plotted.

_U_s_a_g_e:

     spkSlope(object, label = NULL, cuts=c(.6,.99), ...)

_A_r_g_u_m_e_n_t_s:

  object: a SpikeInExpressionSet object

   label: a character string to insert into the plot title

    cuts: quantiles used to make the low, medium, and high bins

     ...: arguments passed to the plot function

_D_e_t_a_i_l_s:

     The bins are created by computing the proportion of non-spike-in
     genes with expression values less than or equal to the average
     expression value at each nominal concentration. Using the default
     value of cuts, the high bin contains nominal concentrations with
     99 percent or more of the non-spike-in expression  values lower
     than it. The medium bin contains nominal concentrations with
     between 60 and 99 percent of the non-spike-in expression values
     lower than it. The low bin contains nominal concentrations with
     less than 60 percent of the non-spike-in expression values lower
     than it.

_V_a_l_u_e:

  avgExp: average expression at each nominal concentration

  slopes: the regression slopes - overall and for each bin

  breaks: which spike-in levels fall in each bin

  brkpts: the expression value of the cut points between bins

    prop: the proportion of non-spike-in probes with expression less
          than the average expression at each nominal concentration

_A_u_t_h_o_r(_s):

     Matthew N. McCall

_E_x_a_m_p_l_e_s:

     data(affy)
     spkSlope(affy)

