maDiagnPlots           package:marrayPlots           R Documentation

_B_a_s_i_c _d_i_a_g_n_o_s_t_i_c _p_l_o_t_s

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

     These three functions produce sets of basic diagnostic plots for
     pre- and post-normalization cDNA microarray data.

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

     maDiagnPlots(mraw, mNorm = NULL, save = TRUE, fname = NULL,
     dev= c("jpeg", "postscript"), pch, col, DEBUG = FALSE, ...)

_A_r_g_u_m_e_n_t_s:

    mraw: Microarray object of class `"marrayRaw"'. By default, plots
          are done for the first array in the batch.

   mNorm: Microarray object of class `"marrayNorm"'. By default, this
          value is NULL and the function maNorm is call to perform
          normalization.

    save: If `TRUE', the figures will be saved to the file named in
          `fname'.

   fname: A "character" string naming the output file.

     dev: A "character" string naming the graphics device, "postscript"
          or "jpeg".

     pch: point style for different control samples.

     col: color code for different control samples.

   DEBUG: If 'TRUE', debug statements are printed.

     ...: Optional graphical parameters, see `par'.

_D_e_t_a_i_l_s:

     'maDiagnPlots' produces plots of pre- and  post-normalization cDNA
     microarray data: color images of log-ratios (M) and
     log-intensities (A) pre- and post-normalization. MA-plots of pre-
     and post-normalization log-ratios M. Log foreground to background
     ratios for both Cy5 and Cy3 channels. Dot plots for replicate
     control spots.

_N_o_t_e:

     This function may not work properly when "save=FALSE".

_A_u_t_h_o_r(_s):

     Yee Hwa (Jean) Yang

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

     'maPlot', 'maImage', 'maBoxplot'

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

     data(swirl)
     ## maDiagnPlots(swirl, dev="postscript", save=TRUE)

