replicatesCV            package:RNAither            R Documentation

_C_o_m_p_u_t_e _t_h_e _c_o_r_r_e_l_a_t_i_o_n _o_f _v_a_r_i_a_t_i_o_n (_C_V)

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

     Computes the correlation of variation as defined in Tseng et al.
     (see References)

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

     replicatesCV(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 to compute the correlation of variation 

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:

     The correlation of variation of an siRNA is defined as the
     standard deviation of its values divided by their mean.

     The function generates a plot of the average intensity against the
     CV for each experiment. The plot will be saved as a pdf and a png
     file named after the experiment name specified in the header
     concatenated with the ' PlotTitle'.

     The function returns a list containing:

histoName : the plotname

minOfScreens : the number of the first experiment

numOfScreens : the number of the last experiment

_R_e_f_e_r_e_n_c_e_s:

     G. C. Tseng et al. Issues in cDNA microarray analysis: quality
     filtering, channel normalization, models of variations and
     assessment of gene effects. Nucleic Acids Res, 29(12): 2549-2557,
     2001.

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

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

     replicatesCV(header, dataset, "Correlation of Variation versus Mean Intensity", 
     "SigIntensity", "GeneName", 1, 0)

