[BioC] Probe IDs from Sentrix chips not appearing in Human annotation file

Mark Dunning mark.dunning at gmail.com
Wed Apr 29 23:51:23 CEST 2009

Hi Nikhil,

Your observations are consistent with what I have seen before with
Illumina data. They have more probes on the array (and in the
bead-level data) than are reported in BeadStudio or in the annotation
files. There could be a few hundred of these. I understand them to be
internal controls of some kind and probably not informative for your

In answer to your other question; the ProbeID column does indeed
correspond to the Array_Address_Id column in the annotation and you
are looking at it the right way. It's unfortunate but probably a
symptom of the way they keep changing the format of their files.

In addition to Marc's response, you could also consider using the
following annotation packages which has these
ProbeIDs/Array_Address_Ids as a key.


Hope this helps. Regards,


On Wed, Apr 29, 2009 at 7:07 PM, Marc Carlson <mcarlson at fhcrc.org> wrote:
> Hi Nikhil,
> What do you have installed?  Can you give us the output of sessionInfo()?
> Since you are using bioconductor, you might want to have a look at the
> annotation package that is maintained for this platform:
> http://www.bioconductor.org/packages/devel/data/annotation/html/illuminaHumanv3.db.html
> If you want some help in how to use that package, you might also look at
> the AnnotationDbi package:
> http://www.bioconductor.org/packages/devel/bioc/html/AnnotationDbi.html
> And finally, if you should discover that your HT platform is
> significantly different from what has been offered by illumina before,
> you could even build a custom annotation package by following the
> instructions in the SQLForge vignette (which you will also find along
> with AnnotationDbi).
>  Marc
> Nikhil Joshi wrote:
>> Hi all,
>> This is my first post, so please bear with me.  I was not able to find
>> any information regarding this in the archives, so I am posting here.
>> I am doing a differential expression analysis using three Human
>> Sentrix chips in R, utilizing the beadarray package.  I am then using
>> the Human annotation file from Illumina (i.e.
>> HumanHT-12_V3_0_R2_11283641_A.txt) to match Probe
>> IDs/Array_address_IDs to GI numbers.  So here are my questions:
>> 1. In R, when I load my data using readIllumina
>> (backgroundMethod="rma", normalizeMethod="quantile",
>> annoPkg="Humanv3"), the data that I get has data for each of the
>> arrays, and within an array there is a column called "ProbeID".
>> However, this ProbeID seems to correspond to the Array_address_ID
>> field in the annotation file, even though there is a field in the
>> annotation file called Probe_Id!  Can anyone explain why the ProbeID
>> in R does NOT correspond to the Probe_Id field in the annotation file,
>> but instead corresponds to the Array_address_Id field?  Am I looking
>> at this incorrectly?
>> 2. After I do my differential expression analysis, I get data for my
>> top results.  These results include a ProbeID field.  Most of these
>> ProbeIDs have entries in the annotation file, however, about 300 do
>> not.  I looked for the probes in the R data, and I found that they did
>> exist and the replication was just as much as all of the other
>> probes.  Which leads me to believe that they are actual probes, and
>> not some error of some kind.  So my question is, why don't these
>> probes have annotation information associated with them in the
>> annotation file?
>> Any help is highly appreciated.  Thank you!
>> - Nik.
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