ebamControl: Further EBAM Arguments
In siggenes: Multiple Testing using SAM and Efron's Empirical Bayes Approaches

Description Usage Arguments Details Value Author(s) References See Also

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

   
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)

`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.

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

A list containing the values of the parameters that are used in ebam or find.a0, respectively.

Holger Schwender, holger.schwender@udo.edu

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.

limma2ebam, ebam, find.a0

siggenes documentation built on Nov. 8, 2020, 6:26 p.m.