Description Usage Arguments Details Value Author(s) References See Also Examples
Given a set of p-values, returns p-values adjusted using one of several methods.
1 | multiple.correction(pval, typeFDR, q)
|
pval |
Vector of pvalues. |
typeFDR |
The correction method. |
q |
The error rate to use for the Two-stages procedure (FDR-TST). |
The multiple correction methods include Bonferroni correction ("FWER"), Benjamini-Hochberg standard false discovery rate correction ("FDR-BH"), Benjamini-Hochberg Adaptive Procedure ("FDR-TST") and the Qvalue procedure (Storey).
A vector of adjusted pvalues.
Nicolas Servant, Eleonore Gravier, Pierre Gestraud, Cecile Laurent, Caroline Paccard, Anne Biton, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupe
- Benjamini Y and Hochberg Y. (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. . Journal of the Royal Statistical Society, Series B, 57: 289-300. - Storey JD. (2002) A direct approach to false discovery rates. Journal of the Royal Statistical Society, Series B, 64: 479-498. - Benjamini Y., Kenigsberg E., Reiner A., Yekutieli D (2005). FDR adjustments of Microarray Experiments.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ## Not run:
## load data
data(marty)
## filtering data
marty <- expFilter(marty, threshold=3.5, graph=FALSE)
##Class label 0/1
marty.type.num <- ifelse(marty.type.cl=="Her2+",0,1)
##Example dataset
example.subset<-marty[1:100,]
## run differential analysis Basal vs HER2+
out <- runTtest(example.subset, labels=marty.type.num, typeFDR="FDR-BH")
## OR :
out2 <- multiple.correction(out$RawpValue, typeFDR="FDR-BH")
## End(Not run)
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