compareReplicates          package:RNAither          R Documentation

_C_o_m_p_a_r_e _r_e_p_l_i_c_a_t_e _v_a_l_u_e_s

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

     Plots replicate intensities pairwise for each experiment.

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

     compareReplicates(header, dataset, plotTitle, col4val, col4anno, 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' 

plotTitle: the plot title 

 col4val: a character string specifying the column whose values will be
          used for the plot 

col4anno: a character string specifying the name of the dataset column
          to be used to define the replicate, e.g. ' "GeneName"' or '
          "Internal_GeneID"' 

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, plots of pairwise comparisons between
     replicate intensities are generated and 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 plot name 

minOfScreens : the number of the first experiment 

numOfScreens : the number of the last experiment 

maxCombinationNum : the number of replicates to compare 

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

     'compareReplicaPlates'

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

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

     compareReplicates(header, dataset, "Comparison of Replicates", "SigIntensity", "GeneName", 1, 0)

