meanSdPlot {vsn} | R Documentation |

## Plot row standard deviations versus row means

### Description

Plot row standard deviations versus row means

### Usage

meanSdPlot(x,
ranks = TRUE,
xlab = ifelse(ranks, "rank(mean)", "mean"),
ylab = "sd",
pch = ".",
col, ...)

### Arguments

`x` |
An object of class `matrix` or
`exprSet` |

`ranks` |
Logical, indicating whether the x-axis (means) should be plotted
on the original scale (FALSE) or on the rank scale (TRUE). The latter
distributes the data more evenly along the x-axis and allows a
better visual assessment of the standard deviation as a function of
the mean. |

`xlab` |
Character, label for the x-axis. |

`ylab` |
Character, label for the y-axis. |

`pch` |
Plot symbol. |

`col` |
Color of plotted points. See details. |

`...` |
Further arguments that get passed to plot.default. |

### Details

Standard deviation and mean are calculated row-wise from the
matrix `exprs(x)`

. The scatterplot of these versus each other
allows to visually verify whether there is
a dependence of the standard deviation (or variance) on the mean.
The red dots depict the running median estimator (window-width 10%).
If there is no variance-mean dependence, then the line formed by the
red dots should be approximately horizontal.

If the `preprocessing`

slot of the `description`

slot of
`x`

is a `list`

and contains an element named
`vsnTrimSelection`

, then the coloring of the points reflects
the trimming that was used in the least trimmed sum of squares (LTS)
estimation (see `vsn`

). If the condition does not apply,
and `col`

is `NULL`

, the points are drawn in black. If
`col`

is not `NULL`

, its value is used for the coloring of
the points.

### Value

The function is called for its side effect, creating a plot on the
active graphics device.

### Author(s)

Wolfgang Huber http://www.ebi.ac.uk/huber

### See Also

`vsn`

### Examples

data(kidney)
log.na = function(x) log(ifelse(x>0, x, NA))
exprs(kidney) = log.na(exprs(kidney))
meanSdPlot(kidney)
## ...try this out with non-logged data, the lymphoma data, your data...

[Package

*vsn* version 1.8.0

Index]