plot.qc.stats {simpleaffy} | R Documentation |
Generates a visual summary of the various QC statistics recommended by Affymetrix in their 'Data Analysis Fundamentals' handbook.
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 |
... |
Other parameters to pass through to plot |
A lot of information is presented in this one figure. The dotted circles correspond to fold-change - the outer one, labelled '+3', corresponds to a 3-fold up-scaling, the middle to no change, and the inner to a 3-fold down-scaling. The blue circle 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 positioning the center of the region so 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 circle 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 they should be within 3. Any that fall outside the three-fold line are coloured red; the rest are blue.
Written around the edge 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 Affymetrix setup.
Finally, if BioB is not present on a chip, this will be flagged by printing 'BioB' in red next to the scale-factor for that chip.
In short, everything in the figure should be blue - red highlights a problem!
Crispin J Miller
## Not run: qc <- qc(eset,eset.mas) plot(qc) ## End(Not run)