Further SAM Arguments

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Description

Specifies most of the optional arguments of sam.

Usage

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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

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