[BioC] TLR4 in illuminaHumanv3.db

[Gavin Koh]

Dear Dr Dunning,

I am looking at Illumina Human WG6 v3 data in an infection and
re-annotated the results using the illuminaHumanv3 package.
After re-annotation, TLR4 disappeared. TLR4 seems to be represented by
only one probe in that array (ILMN_1706217, sequence
GCTGCCACATGTCAGGCCTTATGCTAAGGGTGAGTAATTCCATGGTGCAC). When I BLAT for
that sequence, I get only one hit on chromosome 9 that falls squarely
into the middle of an exon.
I thought I might be using the package incorrectly, but
mget("ILMN_1706217",illuminaHumanv3SYMBOL) returns "NA" and
mget("ILMN_1731048",illuminaHumanv3SYMBOL) gives me "TLR1", which is
correct.

Can you help at all, please? I do not know why the probe seems to have
been marked bad.

Thank you in advance for your time,

Gavin Koh
Team 15, Wellcome Trust Sanger Institute

OSX Snow Leopard
R 2.12.1
illuminaHumanv3.db 1.8.0
illuminaHumanv3() reports
illuminaHumanv3SYMBOL has 25556 mapped keys (of 48803 keys)
DB schema: HUMANCHIP_DB
DB schema version: 2.1
Organism: Homo sapiens