[BioC] Illumina annotation packages discrepancy

Pan Du dupan at northwestern.edu
Mon Dec 1 06:37:39 CET 2008

Hi Renaud,

The reason of discrepancy is due to the different mapping criteria. Both
"lumiHumanAll.db" and "illuminaHumanv2.db" libraries are based on Blasting
result of RefSeq database. The "lumiHumanAll.db" library is nuID indexed and
includes all the probes of different versions. For the mapping from probe to
RefSeq, it defined both sensitivity and specificity (see the vignette
"IlluminaAnnotation.Rnw" in the lumi package). As a result, it might include
less mapping than "illuminaHumanv2.db" because "lumiHumanAll.db" filtered
out some dubious mappings (e.g., one probe has multiple perfect mapping.)

The "lumiHumanV2" library was built based on the original annotation by
Illumina company. As a result, it has much more probe mappings. However,
many mappings might be outdated because of the updates of the genome

Hope this will clarify the confusion.


On 11/28/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Date: Thu, 27 Nov 2008 16:03:36 +0200
> From: Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
> Subject: [BioC] Illumina annotation packages discrepancy
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <492EA8B8.5000400 at cbio.uct.ac.za>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 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

Pan Du, PhD
Research Assistant Professor
Northwestern University Biomedical Informatics Center
750 N. Lake Shore Drive, 11-176
Chicago, IL  60611
Office (312) 503-2360; Fax: (312) 503-5388
dupan (at) northwestern.edu

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