[BioC] Illumina annotation packages discrepancy

Renaud Gaujoux renaud at mancala.cbio.uct.ac.za
Thu Nov 27 15:03:36 CET 2008

Hi list,

I've got BeadSummary data from Illumina (Array content: 
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?


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