R: P-value combination using Fisher's method

fishercomb {metaRNASeq} | R Documentation

## P-value combination using Fisher's method

### Description

Combines one sided p-values using Fisher's method.

### Usage

    fishercomb(indpval, BHth = 0.05)

### Arguments

`indpval` | List of vectors of one sided p-values to be combined.
`BHth` | Benjamini Hochberg threshold. By default, the False Discovery Rate is controlled at 5%.

### Details

The test statistic for each gene g is defined as

F_g = -2 ∑_{s=1}^S ln(p_{gs})

where p_{gs} corresponds to the raw p-value obtained for gene g in a differential analysis for study s (assumed to be uniformly distributed under the null hypothesis). Under the null hypothesis, the test statistic F_g follows a chi-squared distribution with 2S degrees of freedom. Classical procedures for the correction of multiple testing, such as that of Benjamini and Hochberg (1995) may subsequently be applied to the obtained p-values to control the false discovery rate at a desired rate α.

### Value

`DEindices` | Indices of differentially expressed genes at the chosen Benjamini Hochberg threshold.
`TestStatistic` | Vector with test statistics for differential expression in the meta-analysis.
`rawpval` | Vector with raw p-values for differential expression in the meta-analysis.
`adjpval` | Vector with adjusted p-values for differential expression in the meta-analysis.

### References

Y. Benjamini and Y. Hochberg (1995). Controlling the false discovery rate: a pratical and powerful approach to multiple testing. JRSS B (57): 289-300.

M. Brown (1975). A method for combining non-independent, one-sided tests of significance. Biometrics 31(4): 987-992.

A. Rau, G. Marot and F. Jaffrezic (2014). Differential meta-analysis of RNA-seq data. BMC Bioinformatics 15:91

### See Also

`metaRNASeq`

### Examples

    data(rawpval)
    fishcomb <- fishercomb(rawpval, BHth = 0.05)
    DE <- ifelse(fishcomb$adjpval<=0.05,1,0)
    hist(fishcomb$rawpval,nclass=100)

    ## A more detailed example is given in the vignette of the package:
    ## vignette("metaRNASeq")

[Package metaRNASeq version 1.0.2 Index]