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git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50078 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 10/10/2010 23:05:18
Showing 3 changed files

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@@ -569,3 +569,7 @@ function (which expects ff objects and supports parallel processing)
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 2010-10-07 M. Ritchie 1.7.20
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 ** updated vignettes - crlmmIllumina.Rnw and crlmmIllumina.pdf
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 ** tidied code and added snp.index to ffrowapply() in genotype.Illumina() when calls and confidence values are being updated in callSet.
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+2010-10-11 M. Ritchie 1.7.21
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+** fixed bug with indexes for ffrowapply() in genotype.Illumina()
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 Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
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-Version: 1.7.20
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-Date: 2010-10-07
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+Version: 1.7.21
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+Date: 2010-10-11
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 Author: Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry
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 Maintainer: Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
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 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
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@@ -1346,8 +1346,8 @@ processIDAT =  function(sel, sampleSheet=NULL,
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         open(res[["SNR"]])
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         open(res[["mixtureParams"]])
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 	bb = ocProbesets()*length(sns)*8
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-        ffrowapply(A[snp.index,][i1:i2, sel] <- res[["A"]][i1:i2, sel], X=res[["A"]], BATCHBYTES=bb)
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-	ffrowapply(B[snp.index,][i1:i2, sel] <- res[["B"]][i1:i2, sel], X=res[["B"]], BATCHBYTES=bb)
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+        ffrowapply(A[snp.index,][i1:i2, sel] <- res[["A"]][i1:i2, ], X=res[["A"]], BATCHBYTES=bb)
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+	ffrowapply(B[snp.index,][i1:i2, sel] <- res[["B"]][i1:i2, ], X=res[["B"]], BATCHBYTES=bb)
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 	if(length(np.index)>0) {
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           for (j in sel) {
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             A[np.index, j] = res[["cnAB"]]$A[,j]