[BioC] Annotation of Affymetrix hgu133plus2 chip

[Robert Gentleman]

Hi,
 We can only maintain two branches (it is not like we have unlimited
resources), but given that we release twice a year this should not be
 a substantial problem. If you use the devel branch, then you should
 use all of it, all software and data. The devel data packages
 typically do not work with the release branch of the other software
 tools (like Biobase, affy or annotate). 

  This project, like many others relies on user contributions (and
  typically that requires more than just submitting your package, but
  rather doing some of the basic organizational and other work that
  does not get so much credit - writing documentation, as some have
  recently pointed out). If anyone would like to contribute to
  the project, I am sure that we can help them to set up regular
  rebuilds of the release arm, but please don't get the idea that we
  have some enourmous amount of time and manpower that are not being
  used. 

 Robert



On Tue, Aug 31, 2004 at 08:23:00AM -0400, Sean Davis wrote:
> This implies that one needs to use development versions of annotate, 
> GO, etc. to be "compatible"?  Just for clarification....
> 
> On Aug 31, 2004, at 8:17 AM, John Zhang wrote:
> 
> >
> >> Jianhua can correct me, but I think they are updated quarterly, so 
> >> some
> >> of the annotation is likely to have changed.
> >
> > Now we have both the release and developmental tracks that work with 
> > the release
> > and developmental BioC packages, respectively. Only the developmental 
> > track gets
> > updated quartely. To get the devel verion you do:
> >
> >> library(reposTools)
> >> install.packages2(PkgName, develOK = TRUE)
> >
> >
> >>
> >> Sean
> >>
> >> On Aug 31, 2004, at 6:21 AM, Dipl.-Ing. Johannes Rainer wrote:
> >>
> >>> hi,
> >>> does somebody know if the annotation packages for the Affymetrix 
> >>> chips
> >>> will be
> >>> updated sometimes?
> >>> i am using the annotation package hgu133plus2 which was created in
> >>> march and i
> >>> wonder if there may be some changes, for example retired UniGene IDs 
> >>> or
> >>> something like that. I found already a probe set that is annotated to
> >>> GenBank,
> >>> but not on UniGene, although there exists a UniGene cluster with this
> >>> GenBank
> >>> ID.
> >>> thanks to all
> >>>
> >>> _______________________________________________
> >>> Bioconductor mailing list
> >>> Bioconductor at stat.math.ethz.ch
> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor at stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >
> > Jianhua Zhang
> > Department of Biostatistics
> > Dana-Farber Cancer Institute
> > 44 Binney Street
> > Boston, MA 02115-6084
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor

-- 
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| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
| Department of Biostatistics      office: M1B20                            |
| Harvard School of Public Health  email: rgentlem at jimmy.harvard.edu        |
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