MA plot

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Description

Plots of the log2 expression ratios (M values) versus the mean log2 expression values (A values) for each probe for each array.

Usage

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MAplot(x, ...)

## S4 method for signature 'MAList'
MAplot(
    x,
    ...)

## S4 method for signature 'NChannelSet'
MAplot(
    x,
    ...)

Arguments

x

Either an MAList object or an NChannelSet object

...

arguments to pass to xyplot

Details

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.

Methods

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)

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

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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)