Question: annaffy's annotation update
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gravatar for claudio.is@libero.it
14.6 years ago by
claudio.is@libero.it210 wrote:
hi everyone, I would like to have some information about annaffy and in particular about its database. Does it use its own database, or it download information from NCBI, for example to get genbank accession number? if it has its own how often is it updated? thanks in advance Isella Claudio ____________________________________________________________ Libero ADSL: 3 mesi gratis e navighi a 1.2 Mega. E poi hai l'Adsl senza limiti a meno di 1 euro al giorno. Abbonati subito senza costi di attivazione su http://www.libero.it
annaffy • 305 views
ADD COMMENTlink modified 14.6 years ago by rgentleman5.5k • written 14.6 years ago by claudio.is@libero.it210
Answer: annaffy's annotation update
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gravatar for rgentleman
14.6 years ago by
rgentleman5.5k
United States
rgentleman5.5k wrote:
annaffy like most other Bioconductor packages relies on the meta-data packages that are produced and distributed as part of the project. The specific details are contained in the AnnBuilder package that is used to make them. Additionally each meta-data package has QC and build information in it, for example for the hgu95av2 package we get information like: > hgu95av2() Quality control information for hgu95av2 Date built: Wed Sep 15 23:02:49 2004 Number of probes: 12625 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: hgu95av2ACCNUM found 12625 of 12625 hgu95av2CHRLOC found 11382 of 12625 hgu95av2CHR found 12177 of 12625 hgu95av2ENZYME found 1710 of 12625 hgu95av2GENENAME found 12200 of 12625 hgu95av2GO found 10484 of 12625 hgu95av2GRIF found 0 of 12625 hgu95av2LOCUSID found 12302 of 12625 hgu95av2MAP found 12144 of 12625 ... And if you go ?hgu95av2 you will see the actual resources used etc. These are all versioned and typically updated every 3 to 6 months depending on how often the source files are updated. Robert On Jan 15, 2005, at 10:18 AM, claudio..is@@libero..it wrote: > hi everyone, > I would like to have some information about annaffy and in particular > about its > database. Does it use its own database, or it download information > from NCBI, > for example to get genbank accession number? if it has its > own how > often is it updated? > > thanks in advance > > Isella Claudio > > > > ____________________________________________________________ > Libero ADSL: 3 mesi gratis e navighi a 1.2 Mega. E poi hai l'Adsl > senza limiti a meno di 1 euro al giorno. > Abbonati subito senza costi di attivazione su http://www.libero.it > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+
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