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changes in preprocessInfinium2 to accomodate "humanomniexpress12v1b" platform

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/crlmm@49103 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 15:45:18
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@@ -939,28 +939,35 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,
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   SMEDIAN <- getVarInEnv("SMEDIAN")
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   theKnots <- getVarInEnv("theKnots")
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   gns <- getVarInEnv("gns")
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-
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-  # separate out copy number probes
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-  npIndex = getVarInEnv("npProbesFid")
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-  nprobes = length(npIndex)
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   narrays = ncol(XY)
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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)
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-
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-  # new lines below - useful to keep track of zeroed out probes
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-  zero <- matrix(as.integer(exprs(channel(XY, "zero"))[npIndex,]), nprobes, narrays)
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-
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-  colnames(A) <- colnames(B) <- colnames(zero) <- sns
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-  rownames(A) <- rownames(B) <- rownames(zero) <- names(npIndex)
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-  cnAB = list(A=A, B=B, zero=zero, sns=sns, gns=names(npIndex), cdfName=cdfName)
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   if(save.it & !missing(cnFile)) {
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-    t0 <- proc.time()
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-    save(cnAB, file=cnFile)
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-    t0 <- proc.time()-t0
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-    if(verbose) message("Used ", round(t0[3],1), " seconds to save ", cnFile, ".")
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+	  ## separate out copy number probes
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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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+
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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)
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+
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+		  ## new lines below - useful to keep track of zeroed out probes
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+		  zero <- matrix(as.integer(exprs(channel(XY, "zero"))[npIndex,]), nprobes, narrays)
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+
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+		  colnames(A) <- colnames(B) <- colnames(zero) <- sns
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+		  rownames(A) <- rownames(B) <- rownames(zero) <- names(npIndex)
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+
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+		  cnAB = list(A=A, B=B, zero=zero, sns=sns, gns=names(npIndex), cdfName=cdfName)
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+
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+		  t0 <- proc.time()
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+		  save(cnAB, file=cnFile)
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+		  t0 <- proc.time()-t0
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+		  if(verbose) message("Used ", round(t0[3],1), " seconds to save ", cnFile, ".")
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+		  rm(cnAB, B, zero)
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+	  }
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   }
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-  rm(cnAB, B, zero)
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   # next process snp probes
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   snpIndex = getVarInEnv("snpProbesFid")