@@ -569,3 +569,7 @@ function (which expects ff objects and supports parallel processing)

 2010-10-07 M. Ritchie 1.7.20

 ** updated vignettes - crlmmIllumina.Rnw and crlmmIllumina.pdf

 ** tidied code and added snp.index to ffrowapply() in genotype.Illumina() when calls and confidence values are being updated in callSet.

+

+2010-10-11 M. Ritchie 1.7.21

+** fixed bug with indexes for ffrowapply() in genotype.Illumina()

+

@@ -1,8 +1,8 @@

 Package: crlmm

 Type: Package

 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

-Version: 1.7.20

-Date: 2010-10-07

+Version: 1.7.21

+Date: 2010-10-11

 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

 Maintainer: Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

 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

@@ -1346,8 +1346,8 @@ processIDAT =  function(sel, sampleSheet=NULL,

         open(res[["SNR"]])

         open(res[["mixtureParams"]])

 	bb = ocProbesets()*length(sns)*8

-        ffrowapply(A[snp.index,][i1:i2, sel] <- res[["A"]][i1:i2, sel], X=res[["A"]], BATCHBYTES=bb)

-	ffrowapply(B[snp.index,][i1:i2, sel] <- res[["B"]][i1:i2, sel], X=res[["B"]], BATCHBYTES=bb)

+        ffrowapply(A[snp.index,][i1:i2, sel] <- res[["A"]][i1:i2, ], X=res[["A"]], BATCHBYTES=bb)

+	ffrowapply(B[snp.index,][i1:i2, sel] <- res[["B"]][i1:i2, ], X=res[["B"]], BATCHBYTES=bb)

 	if(length(np.index)>0) {

           for (j in sel) {

             A[np.index, j] = res[["cnAB"]]$A[,j]