[BioC] confusion about nomenclature of illumina annotation packages

[Christian Kohler]

Dear list,

I am a bit confused about the nomenclature of the BioC annotation
packages of Illumina BeadChips;
I'm not sure if I am in the know.

Let me take the 'illuminaHumanv2.db' package as an example (mainly the
'v2'-part of the nomenclature), which annotates the Illumina HumanRef-8
BeadChip. Does 'v2' in general indicate the "chip type" (here RefSeq
Bead Chip [if so, then does "v1" stand for WG6 chips?]) or the "chip
version" (HumanRef-8 V2)?
I mean, if it indicates the version, then the packages
'illuminaHumanv1.db' annotates e.g. HumanRef-8 V1.x Bead Chips, right?
But why is the description in BioCViews of 'illuminaHumanv1.db'
"...Illumina HumanRef 6..."?
Another point of confusion is that if I have a dataset where some
samples originate from a Ref8 V1.1 platform and some samples originate
from a Ref8 V2 platform, would it be advisable to annotate the first
samples with the *.v1.db and the latter with the *.v2.db package or can
I use *.v2.db for all samples?
 
I am lost upon these questions.

I am thankful for any help.

Christian


-- 

Christian Kohler
Institute of Functional Genomics
Computational Diagnostics
University of Regensburg (BioPark I)
D-93147 Regensburg (Germany)

Tel. +49 941 943 5055
Fax  +49 941 943 5020
christian.kohler at klinik.uni-regensburg.de