limma to SAM or EBAM

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Description

Transforms the output of an analysis with limma into a SAM or EBAM object, such that a SAM or EBAM analysis, respectively, can be performed using the test statistics provided by limma.

Usage

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limma2sam(fit, coef, moderate = TRUE, sam.control = samControl())

limma2ebam(fit, coef, moderate = TRUE, delta = 0.9, 
   ebam.control = ebamControl())

Arguments

fit

an object of class MArrayLM, i.e.\ the output of the functions eBayes and lmFit from the limma package.

coef

column number or name corresponding to the coefficient or contrast of interest. For details, see the argument coef of the function topTable in limma.

moderate

should the limma t-statistic be considered? If FALSE, the ordinary t-statistic is used in the trasnsformation to a SAM or EBAM object. If TRUE, it is expected that fit is the output of eBayes. Otherwise, fit can be the result of lmFit or eBayes.

sam.control

further arguments for the SAM analysis. See samControl for these arguments, which should only be changed if they are fully understood.

delta

the minimum posterior probability for a gene to be called differentially expressed (or more generally, for a variable to be called significant) in an EBAM analysis. For details, see ebam. Please note that the meaning of delta differs substantially between sam and ebam

ebam.control

further arguments for an EBAM analysis. See ebamControl for these arguments, which should only be changed if their meaning is fully understood.

Value

An object of class SAM or EBAM.

Author(s)

Holger Schwender, holger.schwender@udo.edu

References

Efron, B., Tibshirani, R., Storey, J.D. and Tusher, V. (2001). Empirical Bayes Analysis of a Microarray Experiment. JASA, 96, 1151-1160.

Smyth, G.K. (2004). Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments. Statistical Applications in Genetics and Molecular Biology, 3(1), Article 3.

Tusher, V.G., Tibshirani, R., and Chu, G. (2001). Significance Analysis of Microarrays Applied to the Ionizing Radiation Response. PNAS, 98, 5116-5121.

See Also

sam, ebam, SAM-class, EBAM-class, samControl, ebamControl

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