aqmReportModule
representing the various modules of the quality
report. Given a list of modules, the report
is then rendered by the aqm.writereport
function. Most users will not call these functions directly, but will use the
function arrayQualityMetrics
, which in turns calls these
functions. The function arguments can be provided through the
...
argument of arrayQualityMetrics
.
aqm.boxplot(x, subsample=20000, outlierMethod = "KS", ...)
aqm.density(x, ...)
aqm.heatmap(x, ...)
aqm.pca(x, ...)
aqm.maplot(x, subsample=20000, Dthresh=0.15, maxNumArrays=8, nrColumns=4, ...)
aqm.spatial(x, scale="rank", channels = c("M", "R", "G"), maxNumArrays=8, nrColumns=4, ...)
aqm.meansd(x, ...)
aqm.probesmap(x, ...)# Affymetrix specific sectionsaqm.pmmm(x, ...)
aqm.rnadeg(expressionset, x, ...)
aqm.rle(x, outlierMethod = "KS", ...)
aqm.nuse(x, outlierMethod = "upperquartile", ...)
prepdata(expressionset)
.AffyBatch
.outliers
.maplot
, the arrays with a Hoeffding D
statistic larger than this value are called outliers. See also
hoeffd
.aqm.spatial
, scale
determines the choice of the false colour scale in the
spatial plots. If the value is "rank"
, then the colour is proportional to the
ranks of the values; if it is "direct"
, then it is proportional
to the values themselves. channels
determines for which elements of
x
spatial plots are made.maxNumArrays
determines the number
of arrays for which a plot is produced. nrColumns
determines the number of columns in the
multi-panel plot. In aqm.maplot
, first maxNumArrays
is
incremented to the next multiple of maxNumArrays
. A value of +Inf
is allowed.
If this value is larger than or equal to the actual number of arrays
in x
, then plots are produced for all arrays. If it is smaller,
then plots are shown for the maxNumArrays/2
with the worst
values of Hoeffding's D and for the maxNumArrays/2
best.arrayQualityMetrics
with the same, overall set of arguments.aqmReportModule
.aqm.*
functions, have a
look at the source code of the aqm.pca
function. Please see also
the vignette Advanced topics: Customizing arrayQualityMetrics
reports and programmatic processing of the output.