plot.t2 {sma}R Documentation

Diagnostic Plots for Two-Sample t-statistics

Description

Plots of two-sample t-statistics, |t-numerator| and t-denominator against average A, and plot of |t-numerator| against t-denominator. For each spot on a given slide, A = log_2(R*G)/2, where (R,G) denotes the red and green fluorescence intensity pair. Points with t-statistics exceeding user defined thresholds are highlighted.

Usage

plot.t2(x, main.title="T plots", low=-5, high=5,...)

Arguments

x output from the function stat.t2.
main.title title for the plot.
low lower threshold for t-statistic: points with t<low are colored in green.
high upper threshold for t-statistic: points with t>high are colored in red.
... additional graphical parameters

Author(s)

Sandrine Dudoit, sandrine@stat.berkeley.edu
Yee Hwa Yang, yeehwa@stat.berkeley.edu

See Also

stat.t2, t2stat.func, plot, t.test.

Examples

data(MouseArray)
# mouse.setup <- init.grid()
# mouse.data <- init.data() ## see \emph{init.data}
# mouse.lratio <- stat.ma(mouse.data, mouse.setup)

## Calculation of t-statistics
## cl <- c(rep(1,3), rep(2,3))
## mouse.t2 <- stat.t2(mouse.lratio, cl)

## Diagnostic plots
plot.t2(mouse.t2, "Mouse")

[Package sma version 0.5.15 Index]