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.
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.