Plots of the log2 expression ratios (M values) versus the mean
log2 expression values (A values) for each probe for each array.
Usage
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.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(MmPalateMiRNA)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: xtable
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: statmod
Loading required package: lattice
Loading required package: vsn
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MmPalateMiRNA/MAplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MAplot
> ### Title: MA plot
> ### Aliases: MAplot MAplot-methods MAplot,MAList-method
> ### MAplot,NChannelSet-method
> ### Keywords: methods hplot
>
> ### ** Examples
>
> 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)
>
>
>
>
>
> dev.off()
null device
1
>