sam
.
samControl(delta = NULL, n.delta = 10, p0 = NA, lambda = seq(0, 0.95, 0.05), ncs.value = "max", ncs.weights = NULL, q.version = 1)
NULL
, n.delta
$Delta$ values will be computed automatically.delta
is not specified.NA
, p0
will
be computed by the function pi0.est
.pi0.est
.lambda
is a
vector. Either "max"
or "paper"
. For details, see pi0.est
.lambda
containing the weights used in the estimation of $pi0$. By default
no weights are used. For details, see ?pi0.est
.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
.sam
.
Tusher, V.G., Tibshirani, R., and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. PNAS, 98, 5116-5121.
limma2sam
, sam