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

Marc Carlson mcarlson at fhcrc.org
Wed Apr 29 20:07:49 CEST 2009

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:


If you want some help in how to use that package, you might also look at
the AnnotationDbi package:


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).


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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