Description Usage Arguments Value Note See Also Examples
This function adds 2 lines outlining the pointwise (intensity dependent) confidence band on the M vs A plot. The lines are drawn such that a prespecified proportion of points are outside the 2 confidence curves. The type of line may be specified as well as other parameters.
1 | plot.confband.lines(x, M, crit1=0.025, crit2=crit1, nclass=10, ...)
|
x |
a vector giving the x-coordinates of the points in the scatter plot. In the microarray context, this could be a vector of average log intensities, ie A |
M |
a vector giving the y-coordinates of the points in the scatter plot. In the microarray context, this could be a vector of log intensity ratios. |
crit1 |
The proportion of points less than the lower confidence curve. This takes a decimal value between 0 and 1. |
crit2 |
The proportion of points greater than the upper confidence curve. By default, this has the same value as "crit1". |
nclass |
A single number giving the approximate number of intensity depedent groups to consider. |
... |
graphical parameters may also be supplied as arguments
to the function (see |
Lines are added to the current plot.
An M vs A plot must be constructed prior to the execution of this function.
plot.mva
, stat.ma
,
lines
, matlines
,
plot.confband.text
, plot.confband.points
.
1 2 3 4 5 6 7 8 9 10 11 12 | data(MouseArray)
## mouse.setup <- init.grid
## mouse.data <- init.data
## To display an M vs A plot of the data
plot.mva(mouse.data, mouse.setup)
## Calculate M and A values
mouse.lratio <- stat.ma(mouse.data, mouse.setup)
## To add default upper and lower confidence curves line to the M vs A plot
plot.confband.lines(mouse.lratio$A, mouse.lratio$M)
|
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