Hi list, I've got BeadSummary data from Illumina (Array content: HUMANREF-8_V2_11223162_B.XML.xml). I imported it in R using the function lumi.batch. This automatically computed the nuID for each probe and set the annotation package to lumiHumanAll.db. This is all good. BUT, when I do lookUp(nuIDs, 'lumiHumanAll.db', 'GENENAME') I get 2921out of 20589 probes with NA. If I do the same using the old annotation package lumiHumanV2: lookUp(nuIDs, 'lumiHumanV2', 'GENENAME') I get 454 out of 20589 probes with NA. Finally, if I do the same using the annotation package illuminaHumanv2.db (but based on the corresponding TargetIDs): lookUp(targetIDs, 'illuminaHumanv2.db', 'GENENAME') I get 2041out of 20589 probes with NA. Can anybody give me an explanation for that discrepancy? And what annotation package I should use as it looks like some interesting probes (for my experiment) don't have annotation in the new version? Also I could not find any reference to that HUMANREF-8_V2_11223162_B annotation (neither on Illumina website nor in Bioconductor packages). I only found information about HUMANREF-8_V2_11223162_A. Is the letter suffix (A or B) really important? Thanks