@@ -1,5 +1,5 @@

 Package: GSVA

-Version: 1.39.16

+Version: 1.39.17

 Title: Gene Set Variation Analysis for microarray and RNA-seq data

 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),

              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),

@@ -418,7 +418,6 @@ setMethod("gsva", signature(expr="ExpressionSet", gset.idx.list="GeneSetCollecti

     ## 'annotation' argument

     mapped.gset.idx.list <- mapIdentifiers(gset.idx.list,

                                            AnnoOrEntrezIdentifier(annotpkg))

-    mapped.gset.idx.list <- geneIds(mapped.gset.idx.list) 

   } else {

     mapped.gset.idx.list <- gset.idx.list

     if (verbose) {

@@ -426,6 +425,7 @@ setMethod("gsva", signature(expr="ExpressionSet", gset.idx.list="GeneSetCollecti

         "Attempting to directly match identifiers in 'expr' to gene sets.", sep="\n")

     }

   }

+  mapped.gset.idx.list <- geneIds(mapped.gset.idx.list) 

   ## map to the actual features for which expression data is available

   mapped.gset.idx.list <- .mapGeneSetsToFeatures(mapped.gset.idx.list, rownames(expr))

@@ -486,6 +486,7 @@ setMethod("gsva", signature(expr="matrix", gset.idx.list="GeneSetCollection"),

     mapped.gset.idx.list <- mapIdentifiers(gset.idx.list,

                                            AnnoOrEntrezIdentifier(annotation))

   }

+  mapped.gset.idx.list <- geneIds(mapped.gset.idx.list)

   ## map to the actual features for which expression data is available

   mapped.gset.idx.list <- .mapGeneSetsToFeatures(mapped.gset.idx.list, rownames(expr))

@@ -984,7 +985,7 @@ setMethod("filterGeneSets", signature(gSets="list"),

 setMethod("filterGeneSets", signature(gSets="GeneSetCollection"),

           function(gSets, min.sz=1, max.sz=Inf) {

-  filterGeneSets(geneIds(gSets), min.sz., max.sz)

+  filterGeneSets(geneIds(gSets), min.sz, max.sz)

 })