limma2sam {siggenes} | R Documentation

## limma to SAM or EBAM

### 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

    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`

[Package siggenes version 1.58.0 Index]