maDiagnPlots1          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:

     maDiagnPlots1(mraw, title=NULL, save=TRUE,
             fname=paste(as.character(maLabels(maTargets(mraw))[1]), ".ps", sep = ""), 
             dev=c("postscript", "jpeg"))

     maRawPlots(mraw, title=NULL, save = TRUE, 
             fname = paste(as.character(maLabels(maTargets(mraw))[1]), ".ps", sep = ""), 
             dev = c("postscript", "jpeg"))

     maNormPlots(mnorm, title=NULL, save = TRUE, 
             fname = paste(as.character(maLabels(maTargets(mnorm))[1]),".ps", sep = ""), 
             dev = c("postscript", "jpeg"))

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

    mraw: Microarray object of class '"marrayRaw"', for 'maDiagnPlots1'
          'maRawPlots'. By default, plots are done for the first array
          in the batch.

   mnorm: Microarray object of class '"marrayNorm"', for 'maNormPlots'.
          By default, plots are done for the first array in the batch.

   title: A "character" string for the plot title. If 'NULL' a default
          title is shown.

    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".

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

     'maDiagnPlots1' produces eight plots of pre- and
     post-normalization cDNA microarray data: color images of Cy3 and
     Cy5 background intensities, and of pre- and post-normalization
     log-ratios M; boxplots of pre- and post-normalization log-ratios M
     by print-tip-group; MA-plots of pre- and post-normalization
     log-ratios M by print-tip-group.


     'maRawPlots' produces six plots of pre-normalization cDNA
     microarray data: color images of Cy3 and Cy5 background
     intensities and log-ratios M; boxplots of log-ratios M by
     print-tip-group and plate; MA-plot of log-ratios M by
     print-tip-group.


     'maNormPlots' produces four plots of post-normalization cDNA
     microarray data: color images of location normalization values
     Mloc and normalized log-ratios M; boxplots of normalized
     log-ratios M by print-tip-group; MA-plot of normalized log-ratios
     M by print-tip-group.

_N_o_t_e:

     This function maynot work properly when "save=FALSE".

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

     Sandrine Dudoit, <URL: http://www.stat.berkeley.edu/~sandrine>,
     Yee Hwa (Jean) Yang.

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

     S. Dudoit and Y. H. Yang. (2002). Bioconductor R packages for
     exploratory analysis and normalization of cDNA microarray data. In
     G. Parmigiani, E. S. Garrett, R. A. Irizarry and S. L. Zeger,
     editors, _The Analysis of Gene Expression Data: Methods and
     Software_, Springer, New York.

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

     'maPlot', 'maBoxplot', 'maImage'.

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

     library(marrayNorm)

     # Examples use swirl dataset, for description type ? swirl
     data(swirl)

     maPlate(swirl)<-maCompPlate(swirl,384)

     # Pre-normalization
     maRawPlots(swirl[,3])

     # Post-normalization
     mnorm<-maNorm(swirl[,3], norm="twoD")
     maNormPlots(mnorm, title="Swirl array 93 -- 2D normalization")

