What is the difference between this two annotation files for illumina 450 methylation array?
IlluminaHumanMethylation450kmanifest: annotation files for the 450k array.
IlluminaHumanMethylation450kanno.ilmn12.hg19: annotation files for the 450k array.
Seems that in minfi both are used.
qcReport() calls getManifest(object) that uses ‘IlluminaHumanMethylation450kmanifest’
but
mapToGenome(RSet) uses IlluminaHumanMethylation450kanno.ilmn12.hg19