samControl {siggenes} | R Documentation

## Further SAM Arguments

### Description

Specifies most of the optional arguments of `sam`.

### Usage

    samControl(delta = NULL, n.delta = 10, p0 = NA, lambda = seq(0, 0.95, 0.05),
       ncs.value = "max", ncs.weights = NULL, q.version = 1)

### Arguments

`delta` | a numeric vector specifying a set of values for the threshold Delta that should be used. If `NULL`, `n.delta` Delta values will be computed automatically.
`n.delta` | a numeric value specifying the number of Delta values that will be computed over the range of all possible values for Delta if `delta` is not specified.
`p0` | a numeric value specifying the prior probability pi0 that a gene is not differentially expressed. If `NA`, `p0` will be computed by the function `pi0.est`.
`lambda` | a numeric vector or value specifying the lambda values used in the estimation of the prior probability. For details, see `pi0.est`.
`ncs.value` | a character string. Only used if `lambda` is a vector. Either `"max"` or `"paper"`. For details, see `pi0.est`.
`ncs.weights` | a numerical vector of the same length as `lambda` containing the weights used in the estimation of pi0. By default no weights are used. For details, see `?pi0.est`.
`q.version` | a numeric value indicating which version of the q-value should be computed. If `q.version = 2`, the original version of the q-value, i.e. min{pFDR}, will be computed. If `q.version = 1`, min{FDR} will be used in the calculation of the q-value. Otherwise, the q-value is not computed. For details, see `qvalue.cal`.

### Details

These parameters should only be changed if they are fully understood.

### Value

A list containing the values of the parameters that are used in `sam`.

### Author(s)

Holger Schwender, holger.schwender@udo.edu

### References

Schwender, H., Krause, A., and Ickstadt, K. (2006). Identifying Interesting Genes with siggenes. RNews, 6(5), 45-50.

Storey, J.D. and Tibshirani, R. (2003). Statistical Significance for Genome-Wide Studies. Proceedings of the National Academy of Sciences, 100, 9440-9445.

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

`limma2sam`, `sam`

[Package siggenes version 1.68.0 Index]