I need more precision about annotation of HGU133plus
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@gregory-voisin-945
Last seen 7.8 years ago
Canada
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Ido M. Tamir ▴ 320
@ido-m-tamir-1268
Last seen 8.1 years ago
On Friday 13 April 2007 03:51, gregory voisin wrote: > Hi Bioconductorians, Bioconductoriannes, > My question : on website of bioconductor , I find the package: > hgu133plus2... ( I go in R ...blabla: library (hgu133pluss, then ls > (packages: hgu133plus2).....and here more information than in > affy_annatation file ( I think ).... But this pacakge is developped by > Biocore team core.... Who is Biocore team core? ( on Google, no really a > precise information ) . I would like to know how are these annotations > created, which data origine , which frequency update....??? ?hgu133plus2 HTH ido
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Nianhua Li ▴ 870
@nianhua-li-1606
Last seen 8.1 years ago
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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