ebamControl: Further EBAM Arguments

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

Description

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

Usage

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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



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