[BioC] I need more precision about annotation of HGU133plus

Nianhua Li nli at fhcrc.org
Fri Apr 13 20:43:26 CEST 2007


Hi, Gregory,

The package hgu133plus2 is maintained by our team at the Department of
computational biology at Fred Hutchinson Cancer Research Center at Seattle, WA.
We are part of the biocore team (i.e. the core team of bioconductor). The
package is updated once every six months by using another R package called
AnnBuilder. You can think hgu133plus2 as a product of AnnBuilder. The vignette
of AnnBuilder provides al the details of this package producing process. 

The hgu133plus2 package in bioconductor 2.0 repository was created about a month
ago. All the source data was downloaded on Feb 28, 2007. The lastest Affymetrix
annotation file at that time was dated as Nov 15, 2006 (Affymetrix provides a
newer version on Marth 9). We will update it again about 6 month later, right
before next bioconductor release.

If you think the source data is old, you can always create your own annotation
by using AnnBuilder. You can start from the vignette of AnnBuilder and maybe dig
on the old posts about AnnBuilder on this list.

If you want to use the hgu133plus2 in the repository, I suggest you wait for one
or two weeks. We will provide another version of hgu133plus2 which stores all
data in a sqlite file (google for SQLite). It might be easier for your task. You
can import the sqlite data into a database and do the comparison there without
going through the R layer.

PS: "??? and blabal" is not friendly IMO.

best

nianhua

Nianhua Li
Computational Biology, 
Public Health, Fred Hutchinson Cancer Research Center
Seattle, WA 98109



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