boxplot                package:marray                R Documentation

_B_o_x_p_l_o_t_s _f_o_r _c_D_N_A _m_i_c_r_o_a_r_r_a_y _s_p_o_t _s_t_a_t_i_s_t_i_c_s

_D_e_s_c_r_i_p_t_i_o_n:

     The function 'boxplot' produces boxplots of microarray spot
     statistics for the classes  '"marrayRaw"', '"marrayNorm"'. We
     encourage users to use 'boxplot' rather than 'maBoxplot'. The name
     of the arguments have changed slightly.

_U_s_a_g_e:

     ## S4 method for signature 'marrayRaw':
     boxplot(x, xvar="maPrintTip", yvar="maM", ...)
     ## S4 method for signature 'marrayNorm':
     boxplot(x, xvar="maPrintTip", yvar="maM", ...)

_A_r_g_u_m_e_n_t_s:

       x: Microarray object of class '"marrayRaw"', '"marrayNorm"'

    xvar: Name of accessor method for the spot statistic used to
          stratify the data, typically a slot name for the microarray
          layout object (see '"marrayLayout"') such as 'maPlate' or a
          method such as 'maPrintTip'. If 'x' is NULL, the data are not
          stratified.

    yvar: Name of accessor method for the spot statistic of interest,
          typically a slot name for the microarray object 'm', such as
          'maM'.

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

_D_e_t_a_i_l_s:

     If there are more than one array in the batch, the function
     produces a boxplot for each array in the batch. Such plots are
     useful when assessing the need for between array normalization,
     for example, to deal with scale differences among different
     arrays. Default graphical parameters are chosen for convenience
     using the function 'maDefaultPar' (e.g. color palette,  axis
     labels,  plot title) but the user has the option to overwrite
     these parameters at any point.

_A_u_t_h_o_r(_s):

     Jean Yang and Sandrine Dudoit

_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:

     'maBoxplot', 'maDefaultPar'.

_E_x_a_m_p_l_e_s:

     # To see the demo type demo(marrayPlots)

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

     # Boxplots of pre-normalization log-ratios M for each of the 16 
     # print-tip-groups for the Swirl 93 array. 
     # - Default arguments
     boxplot(swirl[,3])  

     # All spots 
     boxplot(swirl[,3], xvar=NULL, col="green")  

     # Boxplots of pre-normalization red foreground intensities for each grid row
     # for the Swirl 81 array. 
     boxplot(swirl[,1], xvar="maGridRow", yvar = "maRf", main = "Swirl array 81: pre-normalization red foreground intensity") 

     # Boxplots of pre-normalization log-ratios for each array in swirl
     boxplot(swirl, main="Swirl arrays: pre-normalization log-ratios")