makeBoxplotControlsPerPlate     package:RNAither     R Documentation

_G_e_n_e_r_a_t_e _a _b_o_x_p_l_o_t _o_f _t_h_e _d_a_t_a _v_s. _t_h_e _c_o_n_t_r_o_l_s _f_o_r _e_a_c_h _p_l_a_t_e

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

     Generates a boxplot of intensity values of negative controls,
     positive controls and experimental data for each plate of each
     experiment available in the dataset.

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

     makeBoxplotControlsPerPlate(header, dataset, channel, plotTitle, plotDesign, showPlot)

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

  header: the header of a dataset file generated with
          'generateDatasetFile' 

 dataset: an R data frame generated with 'generateDatasetFile' 

 channel: a character string specifying the column whose values will be
          used for the boxplot 

plotTitle: the plot title 

plotDesign: 1 or 2. 1 will generate one window containing all plots, 2
          will generate a series of plots. 

showPlot: 0 or 1. 1 will open one or several plot windows in the R GUI,
          0 will only save the plot(s) without opening windows. 

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

     For each experiment, a series of boxplots of intensity values of
     negative controls, positive controls and experimental data will be
     saved as a pdf and a png file named after the experiment name
     specified in the header concatenated with the ' plotTitle' and the
     number of the experiment.

     The function returns a list containing:

plotName : the plotname

c(minOfScreens, numOfScreens) : a vector with the number of the first
          experiment and of the last experiment

c(minOfPlates, numOfPlates) : a vector with the number of the first
          plate and the number of the last plate

_S_e_e _A_l_s_o:

     'makeBoxplotControls', 'makeBoxplotControlsPerScreen',
     'makeBoxplotPerPlate',  'makeBoxplotPerScreen'

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

     data(exampleHeader, package="RNAither")
     data(exampleDataset, package="RNAither")

     makeBoxplotControlsPerPlate(header, dataset, "SigIntensity", "Data vs. Controls", 1, 1)

