@@ -2,7 +2,7 @@ Package: edge

 Type: Package

 Title: Extraction of Differential Gene Expression

 Date: 2015-04-15

-Version: 2.5.2

+Version: 2.5.3

 Author: John D. Storey, Jeffrey T. Leek and Andrew J. Bass

 Maintainer: John D. Storey <jstorey@princeton.edu>, Andrew J. Bass

     <ajbass@princeton.edu>

@@ -145,10 +145,8 @@ build_study = function(data, grp = NULL, adj.var = NULL, bio.var = NULL,

         fmod <- paste(paste("~", paste(names(pdat)[-1], collapse=" + ")),"+",time.basis,"+", paste( "(", paste(names(pdat)[ncol(pdat)], collapse=" + ", sep=""), ")", ":", time.basis))  }

     }

   }

-  exp_set <- new("ExpressionSet")

   rownames(pdat) <- colnames(data)

-  pData(exp_set) <- data.frame(pdat)

-  exprs(exp_set) <- as.matrix(data)

+  exp_set <- ExpressionSet(as.matrix(data), AnnotatedDataFrame(pdat))

   edgeObj <- deSet(exp_set, full.model=as.formula(fmod),

                      null.model=as.formula(nmod), individual=ind)

   return(edgeObj)

@@ -206,10 +204,7 @@ build_models <- function(data, cov, full.model = NULL, null.model = NULL,

     stop("alternative and null models must be formatted as a formula")

   }

-  exp_set <- new("ExpressionSet")

-  exprs(exp_set) <- data

-  pData(exp_set) <- cov

-

+  exp_set <- ExpressionSet(data, AnnotatedDataFrame(cov))

   edgeObj <- deSet(exp_set, full.model = full.model, null.model = null.model,

                    individual = ind)

   return(edgeObj)