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Changed tolerance allowed for reading in arrays with different numbers of probes (was 10000, now 4% of total number of probes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@91227 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 10/06/2014 23:43:33
Showing3 changed files

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@@ -2,8 +2,8 @@ Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
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-Version: 1.23.0
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-Date: Mon 31 Mar 2014 18:08:54 EST
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+Version: 1.23.1
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+Date: Mon 10 Jun 2014 15:10:27 EST
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 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
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         Ruczinski, Rafael A Irizarry
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 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
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@@ -19,7 +19,7 @@ LinkingTo: preprocessCore (>= 1.17.7)
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 Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
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         1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, SNPchip,
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         utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1),
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-        matrixStats, VGAM
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+        matrixStats, VGAM, parallel
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 Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats,
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         RUnit
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 Collate: AllGenerics.R AllClasses.R methods-AssayData.R methods-CNSet.R
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@@ -77,6 +77,9 @@ import(foreach)
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 importFrom(VGAM, vglm, multinomial, coefficients)
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+importFrom(parallel, makeCluster, detectCores, parRapply, stopCluster, clusterEvalQ)
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+
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+
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 ##----------------------------------------------------------------------------
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 ## export
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 ##----------------------------------------------------------------------------
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@@ -86,7 +86,7 @@ readIdatFiles = function(sampleSheet=NULL,
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 	       headerInfo$ChipType[i] = G$ChipType
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 	       headerInfo$Manifest[i] = G$Unknown$MostlyNull
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 	       headerInfo$Position[i] = G$Unknowns$MostlyA
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-               if(headerInfo$nProbes[i]>(headerInfo$nProbes[1]+10000) || headerInfo$nProbes[i]<(headerInfo$nProbes[1]-10000)) {
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+               if(headerInfo$nProbes[i]>(headerInfo$nProbes[1]+headerInfo$nProbes[1]*0.04) || headerInfo$nProbes[i]<(headerInfo$nProbes[1]-headerInfo$nProbes[1]*0.04)) {
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 		       warning("Chips are not of the same type.  Skipping ", basename(grnidats[i]), " and ", basename(redidats[i]))
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 		       next()
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 	       }