samControl {siggenes} | R Documentation |
Specifies most of the optional arguments of sam
and ebam
.
Currently, only used in limma2sam
and limma2ebam
.
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)
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 . |
These parameters should only be changed if they are fully understood.
A list containing the values of the parameters that are used in sam
or ebam
,
respectively.
Holger Schwender, holger.schwender@udo.edu
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.
limma2sam
, limma2ebam
, sam
, ebam