ebamControl {siggenes} | R Documentation

## Further EBAM Arguments

### Description

Specifies most of the optional arguments of `ebam` and `find.a0`.

### Usage

    ebamControl(p0 = NA, p0.estimation = c("splines", "interval", "adhoc"),
       lambda = NULL, ncs.value = "max", use.weights = FALSE)

    find.a0Control(p0.estimation = c("splines", "adhoc", "interval"),
       lambda = NULL, ncs.value = "max", use.weights = FALSE,
       n.chunk = 5, n.interval = 139, df.ratio = NULL)

### Arguments

`p0` | a numeric value specifying the prior probability p0 that a gene is not differentially expressed. If `NA`, `p0` will be estimated automatically.
`p0.estimation` | either `"splines"` (default), `"interval"`, or `"adhoc"`. If `"splines"`, the spline based method of Storey and Tibshirani (2003) is used to estimate p0. If `"adhoc"` (`"interval"`), the adhoc (interval based) method proposed by Efron et al.\ (2001) is used to estimate p0.
`lambda` | a numeric vector or value specifying the lambda values used in the estimation of p0. If `NULL`, `lambda` is set to `seq(0, 0.95, 0.05)` if `p0.estimation = "splines"`, and to `0.5` if `p0.estimation = "interval"`. Ignored if `p0.estimation = "adhoc"`. For details, see `pi0.est`.
`ncs.value` | a character string. Only used if `p0.estimation = "splines"` and `lambda` is a vector. Either `"max"` or `"paper"`. For details, see `pi0.est`.
`use.weights` | should weights be used in the spline based estimation of p0? If `TRUE`, 1 - `lambda` is used as weights. For details, see `pi0.est`.
`n.chunk` | an integer specifying in how many subsets the `B` permutations should be split when computing the permuted test scores.
`n.interval` | the number of intervals used in the logistic regression with repeated observations for estimating the ratio f0/f.
`df.ratio` | integer specifying the degrees of freedom of the natural cubic spline used in the logistic regression with repeated observations.

### 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 `ebam` or `find.a0`, respectively.

### 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.

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

### See Also

`limma2ebam`, `ebam`, `find.a0`

[Package siggenes version 1.68.0 Index]