How to use the sqlite connection to AnnotationDbi packages

It is very fast and very straightforward:

library(hgu133plus2.db)
hgu133plus2_dbschema()

sql = "
select * from probes p, gene_info g, chromosome_locations c
where g._id=c._id and g._id=p._id limit 10
"

dbGetQuery(hgu133plus2_dbconn(), sql)


If you look at the last few page of the manual for AnnotationDbi [site, PDF], you will see some tips about joining different databases together.