@@ -82,7 +82,7 @@ readIdatFiles = function(sampleSheet=NULL,

 	       headerInfo$ChipType[i] = G$ChipType

 	       headerInfo$Manifest[i] = G$Unknown$MostlyNull

 	       headerInfo$Position[i] = G$Unknowns$MostlyA

-           if(headerInfo$nProbes[i]>(headerInfo$nProbes[1]+10000) || headerInfo$nProbes[i]<(headerInfo$nProbes[1]-10000)) {

+               if(headerInfo$nProbes[i]>(headerInfo$nProbes[1]+10000) || headerInfo$nProbes[i]<(headerInfo$nProbes[1]-10000)) {

 		       warning("Chips are not of the same type.  Skipping ", basename(grnidats[i]), " and ", basename(redidats[i]))

 		       next()

 	       }

@@ -1171,6 +1171,7 @@ genotype.Illumina = function(sampleSheet=NULL,

 	is.lds = ifelse(isPackageLoaded("ff"), TRUE, FALSE)

 	if(missing(cdfName)) stop("must specify cdfName")

 	if(!isValidCdfName(cdfName)) stop("cdfName not valid.  see validCdfNames")

+        pkgname = getCrlmmAnnotationName(cdfName)

 	callSet = construct.Illumina(sampleSheet=sampleSheet, arrayNames=arrayNames,

 			     ids=ids, path=path, arrayInfoColNames=arrayInfoColNames,

                              highDensity=highDensity, sep=sep, fileExt=fileExt, 

@@ -1181,7 +1182,7 @@ genotype.Illumina = function(sampleSheet=NULL,

 	is.snp = isSnp(callSet)

 	snp.index = which(is.snp)

         narrays = ncol(callSet)

-

+        

         if(is.lds) {

           sampleBatches = splitIndicesByNode(seq(along=sampleNames(callSet)))

@@ -1194,7 +1195,7 @@ genotype.Illumina = function(sampleSheet=NULL,

                  sep=sep, fileExt=fileExt, saveDate=saveDate, verbose=verbose, mixtureSampleSize=mixtureSampleSize,

                  fitMixture=fitMixture, eps=eps, seed=seed, cdfName=cdfName, sns=sns, stripNorm=stripNorm,

                  useTarget=useTarget, A=A(callSet), B=B(callSet), SKW=SKW, SNR=SNR,

-                 mixtureParams=mixtureParams, is.snp=is.snp, neededPkgs=c("crlmm", cdfName))

+                 mixtureParams=mixtureParams, is.snp=is.snp, neededPkgs=c("crlmm", pkgname))

           open(SKW)

           open(SNR)