plot.qc.stats           package:simpleaffy           R Documentation

_P_l_o_t_s _a _Q_C_S_t_a_t_s _o_b_j_e_c_t

_D_e_s_c_r_i_p_t_i_o_n:

     Generates a visual summary of the various QC statistics
     recommended by Affymetrix in their 'Data Analysis Fundamentals'
     handbook.

_A_r_g_u_m_e_n_t_s:

       x: A 'QCStats' object 

fc.line.col: The colour to mark fold change lines with 

sf.ok.region: The colour to mark the region in which scale factors lie
          within appropriate bounds 

chip.label.col: The colour to label the chips with 

sf.thresh: Scale factors must be within this fold-range 

gdh.thresh: Gapdh ratios must be within this range 

ba.thresh: beta actin must be within this range 

present.thresh: The percentage of genes called present must lie within
          this range 

bg.thresh: Array backgrounds must lie within this range 

   label: What to call the chips 

    main: The title for the plot 

  usemid: If true use 3'/M ratios for the GAPDH and beta actin probes 

     cex: Value to scale character size by (e.g. 0.5 means that the
          text should be plotted half size) 

     ...: Other parameters to pass through to 'plot' 

_D_e_t_a_i_l_s:

     A lot of information is presented in this one figure. By default,
     each array is represented by a seperate line in the figure. The
     central vertical line corresponds to 0 fold change, the dotted
     lines on either side correspond to 3 fold up and down regulation.
     The blue bar represents the region in which all arrays have scale
     factors within, by default, three-fold of each other. Its position
     is found by calculating the mean scale factor for all chips and
     placing the center of the region such that the borders are -1.5
     fold up or down from the mean value.

     Each array is plotted as a line from the 0-fold line to the point
     that corresponds to its scale factor. If the ends of all of the
     lines are in the blue region, their scale-factors are compatible.
     The lines are coloured blue if OK, red if not.

     The figure also shows GAPDH and beta-actin 3'/5' ratios. These are
     represented as a pair of points for each chip. Affy state that
     beta actin should be within 3, gapdh around 1. Any that fall
     outside these thresholds (1.25 for gapdh) are coloured red; the
     rest are blue.

     Written along the left hand side of the figure are the number of
     genes called present on each array and the average background.
     These will vary according to the samples being processed, and
     Affy's QC suggests simply that they should be similar. If any
     chips have significantly different values this is flagged in red,
     otherwise the numbers are displayed in blue. By default,
     'significant' means that %-present are within 10% of each other;
     background intensity, 20 units. These last numbers are somewhat
     arbitrary and may need some tweaking to find values that suit the
     samples you're dealing with, and the overall nature of your setup.

     Finally, if BioB is not present on a chip, this will be flagged by
     printing 'BioB' in red.

     In short, everything in the figure should be blue - red highlights
     a problem!

_U_s_a_g_e:

     plot.qc.stats(x, fc.line.col = "black", sf.ok.region = "light
     blue", chip.label.col = "black", sf.thresh = 3, gdh.thresh = 1.25,
     ba.thresh = 3, present.thresh = 10, bg.thresh = 20, label =
     NULL,title="QC Stats",spread=c(-8,8),usemid=F,type="l",cex=1, ...)

_A_u_t_h_o_r(_s):

     Crispin J Miller

_S_e_e _A_l_s_o:

     'qc'

_E_x_a_m_p_l_e_s:

       data(qcs)
       plot(qcs)