@@ -1,6 +1,6 @@

 Package: Biobase

 Title: Biobase: Base functions for Bioconductor

-Version: 2.33.0

+Version: 2.33.1

 Author: R. Gentleman, V. Carey, M. Morgan, S. Falcon

 Description: Functions that are needed by many other packages or which

         replace R functions.

@@ -1,3 +1,10 @@

+CHANGES IN VERSION 2.33

+-----------------------

+

+BUG FIXES

+

+    o exprs<- enforces value with correct dim, dimnames.

+

 CHANGES IN VERSION 2.31

 -----------------------

@@ -443,6 +443,26 @@ assayDataElementNames <- function(object) {

 assayDataElement <- function(object, elt) assayData(object)[[elt]]

 assayDataElementReplace <- function(obj, elt, value) {

+    if (!is.null(value) && !identical(unname(dim(obj)), unname(dim(value))))

+        stop("object and replacement value have different dimensions")

+    

+    if (!is.null(value)) {

+        if (!is.null(dimnames(value))) {

+            ## validate and harmonize dimnames

+            vd <- Map(function(od, vd) {

+                if (is.null(vd))

+                    ## update vd to contain indexes into matrix

+                    od <- seq_along(od)

+                else if (!setequal(od, vd))

+                    stop("object and replacement value dimnames differ")

+                od

+            }, dimnames(obj), dimnames(value))

+            ## re-arrange value to have dimnames in same order as obj

+            value <- do.call(`[`, c(list(value), vd, drop=FALSE))

+        }

+        dimnames(value) <- dimnames(obj)

+    }

+

     storage.mode <- storageMode(obj)

     switch(storageMode(obj),

            "lockedEnvironment" = {

@@ -209,10 +209,9 @@ testAssayDataReplacement <- function() {

 testAssayDataElement <- function() {

     checkObj <- function(obj) {

+        m <- new("matrix",0, nr=0, nc=0, dimnames=list(list(),list()))

         checkTrue(identical(assayDataElementNames(obj), "exprs"))

-        checkTrue(identical(assayDataElement(obj, "exprs"),

-                            new("matrix",0,dimnames=list(list(),list()))[FALSE,FALSE,drop=FALSE]))

-        m <- matrix(1:10, nrow=2)

+        checkTrue(identical(assayDataElement(obj, "exprs"), m))

         obj <- assayDataElementReplace(obj, "exprs", m)

         checkTrue(identical(assayDataElement(obj, "exprs"), m))

     }

@@ -295,7 +294,7 @@ testExprs <- function() {

     sNames <- sampleNames(obj)

     oldExprs <- exprs(obj)

     exprs(obj) <- newExprs

-    checkTrue( identical(exprs(obj), newExprs))

+    checkTrue( identical(unname(exprs(obj)), newExprs))

     if (storageMode(obj)!="environment")

       checkTrue(!identical(exprs(obj), oldExprs))

     sampleNames(assayData(obj)) <- sNames

@@ -173,3 +173,17 @@ testHarmonizeAssayDataDimnames <- function() {

     dimnames(se.exprs) <- list(letters[1:5], LETTERS[1:2])

     checkException(checkCreation(exprs, se.exprs), silent=TRUE)

 }

+

+testExprsReplacement <- function() {

+    exprs <- se.exprs <- matrix(1:50, 10, 5)

+    eset <- ExpressionSet(list2env(list(exprs=exprs, se.exprs=se.exprs)))

+    exprs(eset) <- exprs(eset)

+    checkTrue(validObject(eset))

+

+    ## shuffled names ok

+    exprs(eset) <- exprs(eset)[sample(rownames(eset)), sample(colnames(eset))]

+    checkTrue(validObject(eset))

+

+    checkException({ exprs(eset) <- exprs(eset)[, 1:3] }, silent=TRUE)

+    checkException({ exprs(eset) <- exprs(eset)[, c(1:4, 1)] }, silent=TRUE)

+}