plotMAXY              package:beadarray              R Documentation

_S_c_a_t_t_e_r _p_l_o_t_s _a_n_d _M_A-_p_l_o_t_s _f_o_r _a_l_l _s_p_e_c_i_f_i_e_d _a_r_r_a_y_s

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

     Produces scatter and MA-plots for all pairwise comparisons that
     can be made from a set of arrays.

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

     plotMAXY(exprs, arrays, log = TRUE, genesToLabel=NULL,labels=NULL,labelCol="red", labelpch=16,foldLine=2,sampleSize=NULL,...)

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

   exprs: an expression matrix from an ExpressionSet or eSet

  arrays: numeric vector giving the indices of the arrays in BSData we
          want to plot

     log: if TRUE then all values will be log-transformed before
          plotting

genesToLabel: vector specifying names for each array to be plotted

  labels: if TRUE any controls which have been defined in a genes
          object will be plotted

labelCol: specifies a height for the y axis (M values) of the MA-plots.
          Default is 2

labelpch: specifies a height for the y axis (M values) of the MA-plots.
          Default is 2

foldLine: specifies a height for the y axis (M values) of the MA-plots.
          Default is 2

sampleSize: Defines the number of genes to plot.  Default is NULL,
          which plots everything

     ...: other graphical parameters to be passed

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

     These are graphical tools for showing the differences that exist
     between two arrays and they can be used to highlight problems such
     as bias between arrays as well as identifying genes which are
     differentially expressed. We constructed these plots as follows.
     For each bead type, we take the averaged intensity calculated from
     two different arrays. On an XY plot these values are simply
     plotted against each other and on an MA plot we plot the mean of
     the averaged intensities against the corresponding ratio of the
     average intensities.

     In the lower-left section of the plot we see XY plots for all
     pairwise comparisons between the arrays and in the upper right we
     have pairwise MA plots. Going down the first column we observe XY
     plots of array 1 against array 2 and array 1 against array 3 etc.
     Similarly, in the upper-right corner we can observe pairwise MA
     plots.

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

     Mark Dunning

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

     #data(BSData)

     #vec = c (1,2,3)

     #plotMAXY(BSData, vec)

     #BSData = readProbeInfo("my gene list.csv", BSData)

     # Use 'limma' function to read spot types information
     #types = readSpotTypes("control types.csv",sep=",")
     #BSData$genes$Status = controlStatus(types, BSData$genes)

     #plotMAXY(BSData, vec, label=TRUE)

