On Fri, Feb 18, 2011 at 11:41 AM, David Iles <D.E.Iles@leeds.ac.uk> wrote:

> Dear All,
>
> Can anyone point me to a URL where I can obtain an overview of the sources
> of the data incorporated in the current version of hgu133plus2.db? I saw to
> my horror that the actual probesets are based on a really obsolete human
> genome assembly (2003),


What do you mean by "actual probesets"?

The hgu133plus2.db documentation is in the package, for example:

help("hgu133plus2ENTREZID")

Map between Manufacturer Identifiers and Entrez Gene

Description:

     hgu133plus2ENTREZID is an R object that provides mappings between
     manufacturer identifiers and Entrez Gene identifiers.

Details:

     Each manufacturer identifier is mapped to a vector of Entrez Gene
     identifiers. An 'NA' is assigned to those manufacturer identifiers
     that can not be mapped to an Entrez Gene identifier at this time.

     If a given manufacturer identifier can be mapped to different
     Entrez Gene identifiers from various sources, we attempt to select
     the common identifiers. If a concensus cannot be determined, we
     select the smallest identifier.

     Mappings were based on data provided by: Entrez Gene
     ftp://ftp.ncbi.nlm.nih.gov/gene/DATA With a date stamp from the
     source of: 2010-Sep7

References:

     <URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene>

Let us know what additional details are needed, and do note your
sessionInfo()


> sessionInfo()
R version 2.13.0 Under development (unstable) (2011-02-11 r54332)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] hgu133plus2.db_2.4.5  org.Hs.eg.db_2.4.6    RSQLite_0.9-4
[4] DBI_0.2-5             AnnotationDbi_1.13.13 Biobase_2.11.8

loaded via a namespace (and not attached):
[1] tools_2.13.0




> which has changed significantly over the years. As have also genes, gene
> locations, genomic intervals, RefSeq/UniGene entries etcetcetc......
>
> Thanks
>
> Dave
> Dr David Iles
> Institute for Integrative and Comparative Biology
> University of Leeds
> Leeds LS2 9JT
>
> d.e.iles@leeds.ac.uk
>
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