[BioC] Definition of probes in lumiHumanAll annotation database

[Davis, Wade]

Javier,
When you say definition of the probes, do you just mean the sequence of the probes and/or which probes make up a "gene"? Illumina BeadChip arrays consist of only 1 probe when looking at probe-level data. If you are dealing with gene-summarized data (from the old BeadStudio or GenomeStudio), then you are dealing with the average signal over all the probes that map to that gene, but most genes only have 1 probe.

If you want the probe sequence, and you have the nuID (obtained through the lumi package) then you just 'decode' the nuID using this simple webpage:

https://prod.bioinformatics.northwestern.edu/nuID/nuIDoptions.cfm

Then you could using browser/mapping tools to determine if the probe(s) are in a location that would allow you to distinguish isoforms. Based on sheer numbers, I don't think the BeadChip arrays contain nearly enough probes to make this possible for most genes. 

If you want to learn the details of the methodology used to build the lumiHumanAll annotations (and the rest of the lumi*All annotations), a wealth of information is at 
https://prod.bioinformatics.northwestern.edu/nuID/index.cfm

I have used the files and details there to build a custom annotation package.  It really isn't that hard and there are examples on the mailing list. Maybe that is what you need.

Wade




-----Original Message-----
From: Javier Pérez Florido [mailto:jpflorido at gmail.com] 
Sent: Monday, April 02, 2012 2:48 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Definition of probes in lumiHumanAll annotation database

Dear list,
I've checked all the annotation elements given by lumiHumanAll.db and, as far as I know, none of them provides the definition of probes. If I'm not wrong, this definition can distinguishes isoforms and other factors.
How can I get such information from the lumiHumanAll annotation file? 
For example, gene A1CF has three different probes, corresponding each one to a different transcript variant, but I cannot obtain such information from the lumiHumanAll database.

Thanks,
Javier