Description Usage Arguments Details Value Author(s) Examples
Methods for objects of classes
matrix
,
ExpressionSet
,
vsn
and
MAList
to plot row standard deviations versus row means.
1 2 3 4 5 6 7 8 
x 
An object of class

ranks 
Logical, indicating whether the xaxis (means) should be plotted
on the original scale ( 
xlab 
Character, label for the xaxis. 
ylab 
Character, label for the yaxis. 
pch 
Ignored  exists for backward compatibility. 
plot 
Logical. If 
bins 
Gets passed on to 
... 
Further arguments that get passed on to 
Standard deviation and mean are calculated rowwise from the
expression matrix (in) x
. The scatterplot of these versus each other
allows you to visually verify whether there is a dependence of the standard
deviation (or variance) on the mean.
The red line depicts the running median estimator (windowwidth 10%).
If there is no variancemean dependence, then the line should be approximately horizontal.
A named list with five components: its elements px
and
py
are the x and ycoordinates of the individual data points
in the plot; its first and second element are the xcoordinates and values of
the running median estimator (the red line in the plot).
Its element gg
is the plot object (see examples).
Depending on the value of plot
, the method can (and by default does) have a side effect,
which is to print gg
on the active graphics device.
Wolfgang Huber
1 2 3 4 5 6 7 8 9 10 11  data("kidney")
log.na < function(x) log(ifelse(x>0, x, NA))
exprs(kidney) < log.na(exprs(kidney))
msd < meanSdPlot(kidney)
## The `ggplot` object is returned in list element `gg`, here is an example of how to modify the plot
library("ggplot2")
msd$gg + ggtitle("Hello world") + scale_fill_gradient(low = "yellow", high = "darkred") + scale_y_continuous(limits = c(0, 7))
## Try this out with not logtransformed data, vsn2transformed data, the lymphoma data, your data ...

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, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Warning message:
In read.dcf(con) :
URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
Warning message:
Removed 898 rows containing nonfinite values (stat_binhex).
Scale for 'fill' is already present. Adding another scale for 'fill', which
will replace the existing scale.
Warning messages:
1: Removed 898 rows containing nonfinite values (stat_binhex).
2: Removed 49 rows containing missing values (geom_hex).
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.