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

[Nikhil Joshi]

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.

-- 
Nikhil Joshi
Bioinformatics Programmer
UC Davis Genome Center
University of California, Davis
Davis, CA
http://bioinformatics.ucdavis.edu