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

[Macartney, Donia]

Dear Matt

Thanks for replying quickly. 

I don't think (hope) I haven't done anything dumb....

but

I checked controls against my toptable and they didn't overlap. So I definitely have some non-control probes that are missing from the annotation package.

I've also looked at the number of probes in my array data and I have 48,803, and this matches the number in the HT-12 annotation file from Illumina (I'll send you a copy). So I guess the information used to create the annotation file was different. 

How do I go about creating my own annotation package? 

Many thanks for you help

Best wishes

Donia



-----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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