MAplot {MmPalateMiRNA} | R Documentation |
Plots of the log2 expression ratios (M values) versus the mean log2 expression values (A values) for each probe for each array.
MAplot(x, ...) ## S4 method for signature 'MAList' MAplot( x, ...) ## S4 method for signature 'NChannelSet' MAplot( x, ...)
x |
Either an |
... |
arguments to pass to |
The so-called "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.
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)