[BioC] hgu133a annotation and discontinued Entrez IDs

[James W. MacDonald]

David Fermin wrote:
> anna freni sterrantino <annafreni at ...> writes:
> 
>> Hi David ,
>> could be that you should get 
>> library(hgu133a.db)
>> form your sessionInfo it seems that you have the older version.
>> You should also update your R to 2.7 and get the Bioc package Release 2.2.
>>
>> Cheers
>>
>> A.
>>
>>
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> 
> 
> Thank you for your reply. I know there are newer versions available, but for the 
> manuscript I'm preparing I would like to be consistent with version control 
> amongst my analyses.
> 
> The question remains, why am I getting probesets with antiquated Entrez IDs
>  when the annotation package I used (see original message) from August 2007 
> should be adequately up to date so as to exclude these discontinued IDs?

As you noted in your first post, the help page for this package says:

The annotation package was built using a downloadable R package -
AnnBuilder (download and build your own) from www.bioconductor.org
using the following public data sources:
Entrez Gene:ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/. Built: Source data
downloaded from Entrez Gene on Fri Aug 24 18:20:19 2007...

In other words, we downloaded the data from Entrez Gene on that day and 
parsed from there, so any discontinued Entrez Gene IDs in that package 
were still in the data we downloaded and parsed.

Our purpose here is to simply make annotation data available in a 
convenient form, not to check the data made available by NCBI and ensure 
it is correct (that is NCBI's job), so my recommendation would be to 
inform them of these errors.

Best,

Jim



> 
> David
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
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