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

Christian, The v in the illumina annotation package names refer to the Illumina version. I apologize for not describing this better on the Bioconductor site. All versions include the probes for the WG6 formats but the HumanRefSeq8 probes are a subset of WG6 so you can use these annotation packages for either format. Rat does not have a WG6 counterpart. For human, there is v1, v2, and v3. For mouse, there is v1, v1.1, and v2. Because I can't use an extra "." in the name, v1.1 is called illuminaMousev1p1ProbeID.db For rat, there is just v1 so far. You must match the version of your illumina array with version on the annotation package because many if not all the probe IDs will be different. If you have an Illumina Human v2 array, you must use illuminaHumanv2ProbeID.db. I have not seen any Illumina Human chip with a V1.x type of name so I'm not sure what are referring to. Maybe, you are confused with the mouse v1.1 chip? The illuminaHumanv1.db and illuminaHumanv2.db packages were made independently by the Biocore Data team for Illumina Human v1 and v2 chips. They will be a little different than illuminaHumanv1ProbeID.db and illuminaHumanv2ProbeID.db because they used illumina annotation whereas I used results from BLASTing the probe sequences against the current NCBI assembly. They might have also use different probe identifiers than I did. I hope this helps clear up the confusion, Lynn Christian Kohler wrote: > 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 > > >