densityplot {MmPalateMiRNA} | R Documentation |
Plots the estimated density of log2 intensity values for two-color microarrays
## S4 method for signature 'RGList,missing' densityplot( x, channel=c("G", "R"), group=NULL, subset=NULL, ...) ## S4 method for signature 'list,missing' densityplot( x, channel=c("G", "R"), group=NULL, subset=NULL, ...)
x |
Either an |
channel |
The channel to use for calculating distances, one of either "G" (green or control channel) or "R" (red or experimental channel) |
group |
An optional character string specifying the name of a
factor to create separate panel displays, which must be in
|
subset |
An optional character vector specifying the which levels
of |
... |
arguments to pass to |
signature(x = "RGList", data = "missing")
For RGList
objects, separate panel
displays
can be produced for different types of probes, as determined by the
group
argument.
signature(x = "list", data = "missing")
The method for list
objects is intended
to work with lists of normalized data sets, as either
MAList
or
NChannelSet
objects. This
method will produce separate panel displays for each normalized data
set, additionally subsetted by the group
argument if supplied.
The useOuterStrips
function in the latticeExtra package
can be used for ‘outer’ strip labels in the latter case.
D. Sarkar, R. Parkin, S. Wyman, A. Bendoraite, C. Sather, J. Delrow, A. K. Godwin, C. Drescher, W. Huber, R. Gentleman, and M. Tewari. Quality assessment and data analysis for microRNA expression arrays. Nucleic Acids Res, 37(2):e17, 2009.
levelplot
for pairwise distance
plots between arrays,
MADvsMedianPlot
for median
absolute deviation versus median plots, and
MAplot
for MA plots
data(PalateData) res <- densityplot(PalateData, channel="G", group="probe.type", subset = c("Other miRNAs", "MMU miRNAs", "Control"), col=rep(1:3, each=3), lty=rep(1:3, 3), key = list(lines=list(col=rep(1:3, each=3), lty=rep(1:3, 3)), columns=3)) print(res)