compareReplicateSD         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

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

     In the same fashion as 'spatialDistrib', generates a plot of the
     standard deviation of replicate values.

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

     compareReplicateSD(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 a plot of the standard deviation of replicate values of
     all experiments. The plot is saved as a png file named after the
     experiment name specified in the header concatenated with the '
     plotTitle'.

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

     The plot will also be saved as an html file containing mouse-overs
     with the siRNA name for each well.

     The function returns the plotname.

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

     'spatialDistrib', 'compareReplicateSDPerScreen'

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

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

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

