compareReplicateSDPerScreen     package:RNAither     R Documentation

_P_l_o_t _t_h_e _s_t_a_n_d_a_r_d _d_e_v_i_a_t_i_o_n _o_f _r_e_p_l_i_c_a_t_e_s _f_o_r _e_a_c_h _e_x_p_e_r_i_m_e_n_t

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

     In the same fashion as 'spatialDistrib', generates plots of the
     standard deviation of replicate values for each experiment.

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

     compareReplicateSDPerScreen(header, dataset, plotTitle, colname4SD, col4anno, 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 

colname4SD: a character string specifying the column whose values will
          be used for the computation of the replicate standard
          deviation 

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

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:

     Generates plots of the standard deviation of replicate values for
     each experiment. The plots are saved as png files named after the
     experiment name specified in the header concatenated with the '
     plotTitle' and the number of the experiment.

     Wells showing positive controls sd are marked with a "P", wells
     showing negative controls sd with an "N".

     The plots will also be saved as html files containing mouse-overs
     with the siRNA name for each well.

     The function returns a list of length 3 containing: 

basicPlotName : the plot name

minOfScreens : the number of the first experiment

numOfScreens : the number of the last experiment

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

     'spatialDistrib', 'compareReplicateSD'

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

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

     compareReplicateSDPerScreen(header, dataset, "Replicate standard intensity deviation", 
     "SigIntensity", "GeneName", 1)

