\name{lFarms} \alias{lFarms} \title{lFarms expression measure} \description{ This function converts an instance of \code{\link[affy:AffyBatch-class]{AffyBatch}} into an instance of \code{\link[Biobase]{exprSet-class}} using a factor analysis model for which a Bayesian Maximum a Posteriori method optimizes the model parameters under the assumption of Gaussian measurement noise. This function is a wrapper for \code{\link[affy]{expresso}} and uses the function \code{\link[affy]{normalize.loess}} for array normalization. } \usage{ lFarms(object, weight, mu, weighted.mean, laplacian, robust, correction, centering,...) } \arguments{ \item{object}{An instance of \code{\link[affy:AffyBatch-class]{AffyBatch}}.} \item{weight}{Hyperparameter value in the range of [0,1] which determines the influence of the prior. The default value is 0.5 } \item{mu}{Hyperparameter value which allows to quantify different aspects of potential prior knowledge. Values near zero assumes that most genes do not contain a signal, and introduces a bias for loading matrix elements near zero. Default value is 0} \item{weighted.mean}{Boolean flag, that indicates whether a weighted mean or a least square fit is used to summarize the loading matrix. The default value is set to FALSE.} \item{laplacian}{Boolean flag, indicates whether a Laplacian prior for the factor is employed or not. Default value is FALSE.} \item{robust}{Boolean flag, that ensures non-constant results. Default value is TRUE.} \item{correction}{Value that indicates whether the covariance matrix should be corrected for negative eigenvalues which might emerge from the non-negative correlation constraints or not. Default = O (means that no correction is done), 1 (minimal noise (0.0001) is added to the diagonal elements of the covariance matrix to force positive definiteness), 2 (Maximum Likelihood solution to compute the nearest positive definite matrix under the given non-negative correlation constraints of the covariance matrix)} \item{centering}{Indicates whether the data is "median" or "mean" centered. Default value is "median".} \item{...}{other arguments to be passed to \code{\link[affy]{expresso}}.} } \value{\code{\link[Biobase]{exprSet-class}}} \details{ This function is a wrapper for \code{\link[affy]{expresso}}.} \seealso{\code{\link[affy]{expresso}}, \code{\link[farms]{expFarms}}, \code{\link[farms]{qFarms}}, \code{\link[affy]{normalize.loess}}} \examples{ data(testAffyBatch) eset <- qFarms(testAffyBatch) } \keyword{manip}