@@ -344,3 +344,5 @@ is decoded and scanned

  * bug fixed in stripNormalize() [X+16,Y+16 which avoids log(0) = -Inf values, 

       removed inadvertantly in version 1.3.7, put back]

+ * removed header checking from readIdatFiles() (seems to fail often).  

+      Instead check that the number of SNPs agrees (to within +/- 10K SNPs)

@@ -95,7 +95,8 @@ readIdatFiles <- function(sampleSheet=NULL,

 	       headerInfo$ChipType[i] = G$ChipType

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

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

-	       if(headerInfo$ChipType[i]!=headerInfo$ChipType[1] || headerInfo$Manifest[i]!=headerInfo$Manifest[1]) {

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

+                       ## headerInfo$ChipType[i]!=headerInfo$ChipType[1] || headerInfo$Manifest[i]!=headerInfo$Manifest[1]) {

 		       ## || headerInfo$nProbes[i]!=headerInfo$nProbes[1] ## removed this condition as some arrays used the same manifest

 		       ## but differed by a few SNPs for some reason - most of the chip was the same though

 		       ##           stop("Chips are not of all of the same type - please check your data")