samControl: Further SAM Arguments

Description

Specifies most of the optional arguments of sam.

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)

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.

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.

Value

A list containing the values of the parameters that are used in sam.

Details

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

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.