Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/meta_analysis03282012.r

The function can be used to calculate various effect sizes(and the corresponding sampling variances) that are commonly used in meta-analyses.

1 | ```
ind.cal.ES(x, paired, nperm = NULL,miss.tol=0.3)
``` |

`x` |
a list of data sets and their labels. The first list is a list of datasets, the second list is a list of their labels |

`paired` |
A vector of logical values to specify the design patterns of studies. see 'Details'. |

`nperm` |
an integer to specify the number of permutations. |

`miss.tol` |
The maximum percent missing data allowed in any gene (default 30 percent). |

This functions is used to calculate the effect size, standardized mean difference, often used in meta-analysis.

The argument `paired`

is a vector of logical values to specify whether the corresponding study is paired design or
not. If the study is pair-designed, the effect sizes (corresponding variances) are calcualted using the formula in morris's
paper, otherwise calculated using the formulas in choi *et al*.

`ES ` |
The observed effect sizes. |

`Var ` |
The observed variances corresponding to |

`perm.ES` |
The effect sizes calculated from permutations, |

`perm.Var` |
The corresponding variances calculated from permutations. |

Jia Li and Xingbin Wang

Morris SB: Distribution of the standardized mean change effect size for meta-analysis on repeated measures. Br J Math Stat Psychol 2000, 53 ( Pt 1):17-29.

Choi et al, Combining multiple microarray studies and modeling interstudy variation. Bioinformatics,2003, i84-i90.

1 2 3 4 5 6 7 8 | ```
#---example 1: Meta analysis of Differentially expressed genes between two classes----------#
label1<-rep(0:1,each=5)
label2<-rep(0:1,each=5)
exp1<-cbind(matrix(rnorm(5*20),20,5),matrix(rnorm(5*20,2),20,5))
exp2<-cbind(matrix(rnorm(5*20),20,5),matrix(rnorm(5*20,1.5),20,5))
x<-list(list(exp1,label1),list(exp2,label2))
ind.res<-ind.cal.ES(x,paired=rep(FALSE,2),nperm=100)
MetaDE.ES(ind.res,meta.method='REM')
``` |

MetaDE documentation built on May 29, 2017, 9 a.m.

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