samControl {siggenes}R Documentation

SAM and EBAM Arguments

Description

Specifies most of the optional arguments of sam and ebam.

Currently, only used in limma2sam and limma2ebam.

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

Arguments

delta a numeric vector specifying a set of values for the threshold Delta that should be used in sam. If NULL, n.delta Delta values will be computed automatically. Please note that the meaning of the argument delta differs between sam and ebam.
n.delta a numeric value specifying the number of Delta values that will be computed over the range of all possible values for Delta in sam, 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.
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. In the case of samControl, p0.estimation = "splines" is always used. For details on this estimation, see 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 numeric 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. Only considered in samControl.
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. Only considered in ebamControl.
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 or ebam, 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.

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, limma2ebam, sam, ebam


[Package siggenes version 1.18.0 Index]