reprodPlot             package:yaqcaffy             R Documentation

_P_l_o_t _h_u_m_a_n _w_h_o_l_e _g_e_n_o_m_e _G_e_n_e_C_h_i_p_s _r_e_p_r_o_d_u_c_t_i_b_i_l_i_t_y

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

     Compares Affymetrix Human Genome U133 Plus 2.0 Arrays to a subset 
     of the MAQC arrays for a RNA reference.

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

     reprodPlot(userAffyBatchObject,ref,
                       normalize=c("rma","gcrma","mas5","none"),
                       main="MAQC reference reproducibility",
                       cex,...)

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

userAffyBatchObject: a set of Human Genomue U133 Plus 2.0 arrays 
          provided as an AffBatch object,

     ref: a string ("refA", "refB", "refC", or "refD") defining the RNA
           reference to compare the userAffyBatchObject to,

normalize: a string defining the algorithm used for data normalization:
           'rma' (default) for RMA (as imlplemented in the 'affy'
          library),  'gcrma' for GCRMA (as imlplemented in the 'gcrma'
          library),  'mas5' for MAS5 (as imlplemented in the 'affy'
          library)  or 'none' for no normalization,

    main: an overall title for the plot,

     cex: size of text on the plot,

     ...: other arguments.

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

     The plot shows all the pairwise scatterplots (plotted with 
     geneplotter)'s 'smoothScatter' function)  with Pearson's
     correlation factor and MAplots (plotted with  affy's 'ma.plot'
     function). The subset of the MAQC arrays are 1 randomly chosen
     .CEL file out  of the 5 replicates for the 6 different test site.

_V_a_l_u_e:

     Outputs a graph on the available graphical device

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

     Laurent Gatto

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

      ## Not run: 
        ## loading data
        library(MAQCsubsetAFX)
        data(refB)
        d<-refB[,1]
        ## testing the reproductibility against ref A
        reprodPlot(d,"refA",normalize="rma")
      
     ## End(Not run)

