Plots of the log2 expression ratios (M values) versus the mean log2 expression values (A values) for each probe for each array.
1 2 3 4 5 6 7 8 9 10 11 
x 
Either an 
... 
arguments to pass to 
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.
signature(x = "MAList")
M
and A
values are stored as matrices in x
signature(x = "NChannelSet")
M
and A
values are calculated from the R
and
G
matrices returned by assayData(x)
densityplot
for density plots
of log2 intensity values,
levelplot
for pairwise distance
plots between arrays,
and MADvsMedianPlot
for median
absolute deviation versus median plots.
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)

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