metaRNASeq (version 0.4)

fishercomb: 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%.

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.

Details

The test statistic for each gene g is defined as $$F_g = -2 \sum_{s=1}^S ln(p_{gs})$$ 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 $\chi^2$ 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 $\alpha$.

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 (2012). Differential meta-analysis of RNA-seq data. (Manuscript in progress)

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")