@@ -59,7 +59,7 @@ Collate:

     'utils.R'

     'zzz.R'

 Depends:

-    R (>= 2.16.0),flowCore(>= 1.45.2),ncdfFlow(>= 2.19.5)

+    R (>= 2.16.0),flowCore(>= 1.45.14),ncdfFlow(>= 2.25.4)

 biocViews: FlowCytometry, DataImport, Preprocessing, DataRepresentation

 Suggests:

     testthat,

@@ -304,8 +304,15 @@ load_gs<-function(path){

         }

       }

-       

-

+      trans <- gs@transformation

+      if(length(trans)!=0)

+      {

+        if(is(trans , "transformerList")){

+          gs@transformation <- sapply(sampleNames(gs), function(sn)trans, simplify = FALSE)

+        }

+        

+      }

+      

       message("Done")

       list(gs=gs,files=c(dat.file,rds.file))

 }

@@ -1935,6 +1942,7 @@ setMethod("[",c("GatingSet"),function(x,i,j,...,drop){

             #copy the R structure

             clone <- x

             clone@axis <- clone@axis[i]

+            clone@transformation <- clone@transformation[i]

             #subsetting data

 			fs <- flowData(clone)[i]

@@ -2045,7 +2053,7 @@ setMethod("[[",c(x="GatingSet",i="character"),function(x,i,j,...){

                             , flag = x@flag

                             , axis = x@axis

                             , guid = x@guid

-                            , transformation = x@transformation

+                            , transformation = x@transformation[[i]]

                             , compensation = x@compensation

                             , name = i)

@@ -2251,7 +2259,7 @@ setMethod("keyword",c("GatingSet","character"),function(object,keyword){

 #' is supported.

 #'

 #' @param _data \code{GatingSet} or \code{GatingSetList}

-#' @param translist expect a \code{transformList} object

+#' @param translist expect a \code{transformList} object or a list of \code{transformList} objects(with names matched to sample names)

 #' @param ... other arguments passed to 'transform' method for 'ncdfFlowSet'.(e.g. 'ncdfFile')

 #' @return a \code{GatingSet} or \code{GatingSetList} object with the underling flow data transformed.

 #' @examples

@@ -2279,13 +2287,29 @@ setMethod("transform",

     {

       gs <- `_data`

-      if(missing(translist)||!is(translist, "transformerList"))

-        stop("expect the second argument as a 'transformerList' object!")

+      

+      if(missing(translist))

+        stop("Missing the second argument 'translist'!")

+      else if(is(translist, "transformerList"))

+      {

+        translist <- sapply(sampleNames(gs), function(obj)translist, simplify = FALSE)

+      }

+      

+      if(is(translist, "list"))

+      {

+        tList <- lapply(translist, function(trans){

+          if(!is(trans, "transformerList"))

+            stop("All the elements of 'translist' must be 'transformerList' objects!")

+          

+          res <- lapply(trans, function(obj)obj[["transform"]])

+          transformList(names(trans), res)  

+        })

+      }else

+        stop("expect the second argument as a 'transformerList' object or a list of 'transformerList' objects!")

       gs@transformation <- translist

       fs <- getData(gs)

-      tList <- lapply(translist, function(obj)obj[["transform"]])

-      tList <- transformList(names(translist), tList)

+      

       suppressMessages(fs_trans <- transform(fs, tList, ...))

       flowData(gs) <- fs_trans

       gs

@@ -13,7 +13,7 @@

 \arguments{

 \item{_data}{\code{GatingSet} or \code{GatingSetList}}

-\item{translist}{expect a \code{transformList} object}

+\item{translist}{expect a \code{transformList} object or a list of \code{transformList} objects(with names matched to sample names)}

 \item{...}{other arguments passed to 'transform' method for 'ncdfFlowSet'.(e.g. 'ncdfFile')}

 }

@@ -64,11 +64,13 @@ test_that("compensate & transform a GatingSet", {

       transObj <- estimateLogicle(gs[[1]], c("FL1-H", "FL2-H"))

-      expect_error(gs.trans <- transform(gs), regexp = "transformerList")

+      expect_error(gs.trans <- transform(gs), "Missing the second argument")

       expect_error(gs.trans <- transform(gs, translist), regexp = "transformerList")

       suppressMessages(gs.trans <- transform(gs, transObj))

-      expect_equal(gs.trans@transformation, transObj)

+      transObj.list <- sapply(sampleNames(gs), function(obj)transObj, simplify = FALSE)

+      

+      expect_equal(gs.trans@transformation, transObj.list)

       fs.trans.gs <- getData(gs.trans)

       expect_equal(fsApply(fs.trans.gs, colMeans, use.exprs = TRUE), expectRes)

@@ -78,4 +80,4 @@ test_that("compensate & transform a GatingSet", {

       fs.trans.gs <- getData(gs.trans)

       expect_equal(fsApply(fs.trans.gs, colMeans, use.exprs = TRUE), expectRes)

       expect_equal(fs.trans.gs@file, tmp)

-    })

\ No newline at end of file

+    })