MA plot
Description
Plots of the log2 expression ratios (M values) versus the mean log2 expression values (A values) for each probe for each array.
Usage
1 2 3 4 5 6 7 8 9 10 11 
Arguments
x 
Either an 
... 
arguments to pass to 
Details
The socalled "MA" plot can be used to evaluate whether their is a bias associated with overall intenstity level for each array. Loess smoothed regression lines are superimposed on each plot to demonstrate the trend.
Methods
signature(x = "MAList")

M
andA
values are stored as matrices inx
signature(x = "NChannelSet")

M
andA
values are calculated from theR
andG
matrices returned byassayData(x)
See Also
densityplot
for density plots
of log2 intensity values,
levelplot
for pairwise distance
plots between arrays,
and MADvsMedianPlot
for median
absolute deviation versus median plots.
Examples
1 2 3 4 5 6  data(PalateData)
reducedSet < filterArray(PalateData, keep=c("MIR", "LET", "POSCON", "CALIB"),
frac=1.1, number=3, reps=4)
ndata.quantile < normalizeBetweenArrays(reducedSet, method="quantile")
res < MAplot(ndata.quantile)
print(res)
