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git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50028 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 08/10/2010 06:08:35
Showing1 changed files

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@@ -82,7 +82,7 @@ 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]+10000) || headerInfo$nProbes[i]<(headerInfo$nProbes[1]-10000)) {
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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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 	       }
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@@ -1171,6 +1171,7 @@ genotype.Illumina = function(sampleSheet=NULL,
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 	is.lds = ifelse(isPackageLoaded("ff"), TRUE, FALSE)
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 	if(missing(cdfName)) stop("must specify cdfName")
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 	if(!isValidCdfName(cdfName)) stop("cdfName not valid.  see validCdfNames")
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+        pkgname = getCrlmmAnnotationName(cdfName)
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 	callSet = construct.Illumina(sampleSheet=sampleSheet, arrayNames=arrayNames,
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 			     ids=ids, path=path, arrayInfoColNames=arrayInfoColNames,
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                              highDensity=highDensity, sep=sep, fileExt=fileExt, 
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@@ -1181,7 +1182,7 @@ genotype.Illumina = function(sampleSheet=NULL,
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 	is.snp = isSnp(callSet)
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 	snp.index = which(is.snp)
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         narrays = ncol(callSet)
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-
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+        
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         if(is.lds) {
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           sampleBatches = splitIndicesByNode(seq(along=sampleNames(callSet)))
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@@ -1194,7 +1195,7 @@ genotype.Illumina = function(sampleSheet=NULL,
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                  sep=sep, fileExt=fileExt, saveDate=saveDate, verbose=verbose, mixtureSampleSize=mixtureSampleSize,
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                  fitMixture=fitMixture, eps=eps, seed=seed, cdfName=cdfName, sns=sns, stripNorm=stripNorm,
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                  useTarget=useTarget, A=A(callSet), B=B(callSet), SKW=SKW, SNR=SNR,
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-                 mixtureParams=mixtureParams, is.snp=is.snp, neededPkgs=c("crlmm", cdfName))
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+                 mixtureParams=mixtureParams, is.snp=is.snp, neededPkgs=c("crlmm", pkgname))
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           open(SKW)
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           open(SNR)