stat.t2 {sma} | R Documentation |

## Two-sample t-statistics

### Description

Computes two-sample t-statistics for each gene in a multi-slide
microarray experiment.

### Usage

stat.t2(X, cl, x.ratio=FALSE, var.equal=TRUE, ...)

### Arguments

`X` |
if x.ratio=F, X is a list containing two components. The
first component is a matrix of log intensity ratios
*M=log_2 (R/G)* and the second component is the
average log intensities *A =
log_2(R*G)/2*, such as the output
from `stat.ma` . If x.ratio=T, X is a matrix of log
expression ratios only. The rows of X correspond to genes and
columns correspond to different hybridizations, that is different
slides. |

`cl` |
vector of class labels. Must consist of integers 1 and 2. |

`x.ratio` |
logical flag: if TRUE, the matrix X contains only
log intensity ratios, if FALSE, X is a list containing two
components. The first component is a matrix of log expression
ratios and the second component contains average log
intensities A. |

`var.equal` |
logical flag: if TRUE, the variances of the class
1 and class 2 parent populations are assumed equal. |

`...` |
other parameters used in `t.test` . |

### Value

List containing the following components

`t` |
the two-sample t-statistic for each gene; |

`Num ` |
the numerator of the t-statistic for each gene, with
names attribute "Num"; |

`Denominator` |
the denominator of the t-statistic for each gene, with
names attribute "Den"; |

`n1` |
number of class 1 observations used to calculate the
t-statistic for each gene; |

`n2` |
number of class 2 observations used to calculate the
t-statistics for each gene; |

`Average A` |
if x.ratio=F, the average across all
hybridizations of *A = log_2(R*G)/2*,
with names attribute "A.bar", if x.ratio=T, NULL is returned. |

### Note

`t2stat.func`

is called by `stat.t2`

and is not typically used on its own.

### Author(s)

Sandrine Dudoit, sandrine@stat.berkeley.edu

Yee Hwa Yang, yeehwa@stat.berkeley.edu

### References

D. Freedman, R. Pisani, and
R. Purves. (1998). Statistics, 3rd ed. NewYork: W.W. Norton.

### See Also

`t2stat.func`

, `plot.t2`

,
`plot.qq`

, `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)
cl <- c(rep(1,3), rep(2,3))
mouse.t2 <- stat.t2(mouse.lratio, cl)

[Package

*sma* version 0.5.15

Index]