[BioC] Does illuminaHumanv3BeadID.db correspond to the Illumina HT-12 chip

Mark Dunning mark.dunning at gmail.com
Tue Nov 17 15:45:32 CET 2009


Hi Donia,

I checked the IDs you sent me off the BioC list. All except two are
classed as "Bad" by our recent re-annotation of the platform, meaning
they are unlikely to accurately measure the target that they were
designed for. You can search such details at our website

http://remoat.sysbiol.cam.ac.uk/

The other two IDs have no RefSeq symbol associated so will not be annotated.

Nevertheless, I did find some probes that were missing from the
annotation package that should not have been, so I will be uploading a
new version to BioC very soon.

Regards,

Mark

>>> -----Original Message-----
>>> From: Matthew Ritchie [mailto:mritchie at wehi.EDU.AU]
>>> Sent: Wednesday, 11 November 2009 1:57 p.m.
>>> To: Macartney, Donia
>>> Cc: bioconductor at stat.math.ethz.ch
>>> Subject: Re: [BioC] Does illuminaHumanv3BeadID.db correspond to the
>>> Illumina HT-12 chip
>>>
>>> Dear Donia,
>>>
>>>> Sorry if I've missed this somewhere
>>>>
>>>> I'm analysing new data from an Human Illumina HT-12 v3 BeadChip. I'm
>>>> using BeadID as the identifier however the  illuminaHumanv3BeadID.db
>>>> package seems to be missing some of the Bead Ids from my top table
>>>> list. Is there a different package I can use - or what packages
>>>> should I use to create my own annotation package?
>>>
>>> You are using the correct package.  Note that this annotation package (and most others available from BioC) only contains information for non-control probes.  Maybe the probes in question are controls?  You can get a list of control BeadIDs for Human v3 chips using the following commands - check to see whether any of these match up with the ones in your top table.
>>>
>>> library(beadarray)
>>> data(ExpressionControlData)
>>> ExpressionControlData$Humanv3[,1]
>>>
>>> I hope this helps.  Best wishes,
>>>
>>> Matt
>>>
>>>
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