empiricalStart {XDE} | R Documentation |
Empirical starting values for the MCMC are based on data in objects of
class ExpressionSetList
empiricalStart(object, zeroNu = FALSE, phenotypeLabel, one.delta=FALSE, T_THRESH=4)
object |
An object of class ExpressionSetList |
zeroNu |
Logical: if TRUE, the nu in the Bayesian model are not modeled – set to zero and not updated in the MCMC. Setting zeroNu to TRUE should be regarded as experimental |
phenotypeLabel |
character: binary phenotype. phenotypeLabel must be in the varLabels of each ExpressionSet object |
one.delta |
delta in the Bayesian model is a gene-specific indicator for differential expression. If one.delta is FALSE, we assume that a gene can be differentially expressed in a subset of studies. When TRUE, we assume that a gene is differentially expressed in all studies or in none. |
T_THRESH |
A threshold of t-statistics (calculated row-wise for each study) for determining starting values of the differential expression indicator, delta. |
A list containing starting values for the MCMC that are derived from empirical estimates of the data.
R. Scharpf
zeroNu
, XdeParameter-class
,
ExpressionSetList-class
data(expressionSetList) eList <- studyCenter(expressionSetList) empirical <- empiricalStart(eList, phenotypeLabel="adenoVsquamous", T_THRESH=3) ##By default, initial values for the MCMC are sampled from the prior ##when initializing an object of class XdeParamater params <- new("XdeParameter", esetList=eList, phenotypeLabel="adenoVsquamous", one.delta=FALSE, burnin=TRUE) ##The initial values can be replaced by empirical values as follows: firstMcmc(params) <- empirical