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Added a checks to see whether XY@assayData$X is 'ff' or 'ffdf' in preprocessInfinium2

Added the following line:
is.ff <- is(XY@assayData$X, "ff") | is(XY@assayData$X, "ffdf")

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/crlmm@49106 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 15:45:24
Showing1 changed files

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@@ -946,9 +946,12 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,
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 	  npIndex = getVarInEnv("npProbesFid")
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 	  nprobes = length(npIndex)
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 	  if(length(nprobes > 0)){
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-		  open(XY@assayData$X)
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-		  open(XY@assayData$Y)
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-		  open(XY@assayData$zero)
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+		  is.ff <- is(XY@assayData$X, "ff") | is(XY@assayData$X, "ffdf")
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+		  if(is.ff){
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+			  open(XY@assayData$X)
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+			  open(XY@assayData$Y)
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+			  open(XY@assayData$zero)
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+		  }
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 		  A <- matrix(as.integer(exprs(channel(XY, "X"))[npIndex,]), nprobes, narrays)
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 		  B <- matrix(as.integer(exprs(channel(XY, "Y"))[npIndex,]), nprobes, narrays)