dyeswapfilter            package:maanova            R Documentation

_G_e_n_e _f_i_l_t_e_r _f_o_r _d_y_e-_s_w_a_p _e_x_p_e_r_i_m_e_n_t

_D_e_s_c_r_i_p_t_i_o_n:

     This function is used to flag the questionable spot in any kind of
     dye-swap experiment.

     This function only works for 2-dye arrays.

_U_s_a_g_e:

     dyeswapfilter(dataobj, r=4)

_A_r_g_u_m_e_n_t_s:

 dataobj: An object of class 'madata'.

       r: A cut-off value for bad spot. The genes with log-ratio
          difference larger than r times standard deviation will be
          flagged.

_D_e_t_a_i_l_s:

     For each pair of dye-swap, the difference in log ratios (d) are
     computed. Then compute the IQR (interquartile range) of d and
     convert that to Standard Deviation by SD = IQR/1.35. Any gene with
     d larger than r times SD will be flagged.

     Note that I assume in the input data object, the adjacent arrays
     is a dye-swap pair.

_V_a_l_u_e:

     An object of class 'rawdata' or 'madata' with the 'flag' field
     created or updated.

_A_u_t_h_o_r(_s):

     Hao Wu

_E_x_a_m_p_l_e_s:

     ## Not run: 
     data(kidney)
     # riplot before filtering
     riplot(kidney.raw, array=1)
     # filter the gene
     rawdata <- dyeswapfilter(kidney.raw)
     # riplot again - some genes are highlighted
     riplot(rawdata, array=1)
     ## End(Not run)

