@@ -1,10 +1,10 @@

 Package: convert

-Version: 1.31.0

+Version: 1.31.1

 Title: Convert Microarray Data Objects

-Author: Gordon Smyth <smyth@wehi.edu.au>, 

-	James Wettenhall <wettenhall@wehi.edu.au>, 

-	Yee Hwa (Jean Yang) <jean@biostat.ucsf.edu>, 

-	Martin Morgan <mtmorgan@fhcrc.org>Martin Morgan 

+Author: Gordon Smyth <smyth@wehi.edu.au>,

+	James Wettenhall <wettenhall@wehi.edu.au>,

+	Yee Hwa (Jean Yang) <jean@biostat.ucsf.edu>,

+	Martin Morgan <mtmorgan@fhcrc.org>Martin Morgan

 Maintainer: Yee Hwa (Jean) Yang <jean@biostat.ucsf.edu>

 Depends: R (>= 2.6.0), Biobase (>= 1.15.33), limma (>= 1.7.0), marray, utils, methods

 Description: Define coerce methods for microarray data objects.

@@ -108,11 +108,14 @@ setAs("MAList", "ExpressionSet", function(from)

 #  Robert Gentleman

 #  22 November 2006

 {

-    nM <- new("MIAME")

-    notes(nM) <- list("Converted from MAList object, exprs are M-values")

-    new("ExpressionSet", exprs = as.matrix(from$M),

-        phenoData = new("AnnotatedDataFrame", data=from$targets),

-        experimentData = nM)

+    theExperimentData <- new("MIAME")

+    notes(theExperimentData) <- list("Converted from MAList object, exprs are M-values")

+    theExprs <- as.matrix(from$M)

+    thePhenoData <- from$targets

+    rownames(thePhenoData) <- colnames(theExprs)

+    new("ExpressionSet", exprs = theExprs,

+        phenoData = new("AnnotatedDataFrame", data=thePhenoData),

+        experimentData = theExperimentData)

 })