[BioC] AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)

[Luo Weijun]

Thank you, John. Shall I use 2-column or 3-column base
file for the new version of AnnBuilder? And the new
version number will be 1.10.2 or 1.10.3? I have
already seen an OS X binary version shown up in
AnnBuilder website,
http://www.bioconductor.org/packages/bioc/1.8/html/AnnBuilder.html,
 I am not sure whether that's the new version.
Weijun

--- John Zhang <jzhang at jimmy.harvard.edu> wrote:

> 
> >I installed the updated version of AnnBuilder
> >successfully following your suggestion. The bad
> news
> >is that I still don¡¯t have the gene information,
> >xxACCNUM, xxGENENAME, xxSYMBOL,
> >xxGO, xxOMIM, xxPMID, etc, in my built annotation
> >package, after I inserted one empty column between
> >probe names and Entrez Gene ID columns in my base
> >file. Here is what I got: 
> 
> I have fixed the code. You may want to wait to use
> the new version off the 
> developmental track.
> 
> 
> 
> >
> >> library(hs95av2Entrezg7)
> >> hs95av2Entrezg7()
> >
> >
> >Quality control information for  hs95av2Entrezg7 
> >Date built: Created: Thu Jul 13 12:25:38 2006  
> > 
> >Number of probes: 8359 
> >Probe number missmatch: None 
> >Probe missmatch: None 
> >Mappings found for probe based rda files: 
> >         hs95av2Entrezg7ACCNUM found 0 of 8359
> >         hs95av2Entrezg7CHRLOC found 8042 of 8359
> >         hs95av2Entrezg7ENZYME found 1315 of 8359
> >         hs95av2Entrezg7LOCUSID found 8292 of 8359
> >         hs95av2Entrezg7PATH found 2785 of 8359 
> >Mappings found for non-probe based rda files:
> >         hs95av2Entrezg7CHRLENGTHS found 25
> >         hs95av2Entrezg7ENZYME2PROBE found 652
> >         hs95av2Entrezg7ORGANISM found 1
> >         hs95av2Entrezg7PATH2PROBE found 180
> >         hs95av2Entrezg7PFAM found 6934
> >         hs95av2Entrezg7PROSITE found 4941 
> >
>
>>a=read.delim('/Users/luow/project/microarraydata/annotation/hs95av2Entrezg7Bas
> e.txt',sep='\t',
> >head=F)
> >> head(a)
> >        V1 V2    V3
> >1 10001_at NA 10001
> >2 10002_at NA 10002
> >3 10003_at NA 10003
> >4 10004_at NA 10004
> >5 10005_at NA 10005
> >6 10006_at NA 10006
> >>
> >Below is my sessionInfo when I build the
> annotation.
> >Actually before I updated AnnBuilder, the same
> thing
> >happened when I used a 3-column base file. It seems
> to
> >me that to get those gene information data, our
> >current llParser needs GenBank accession numbers in
> >the 2nd column. But it doesn¡¯t make too much sense
> to
> >me, since to pull out gene information from NCBI
> >Entrez Gene database, we just need any one of the
> >commonly used gene IDs¡­
> >Please let me know what I can do about this. Thank
> you
> >again for all your kind help.
> >Weijun
> >
> >> sessionInfo()
> >Version 2.3.1 (2006-06-01) 
> >powerpc-apple-darwin8.6.0 
> >
> >attached base packages:
> >[1] "tools"     "methods"   "stats"     "graphics" 
> >"grDevices" "utils"    
> >[7] "datasets"  "base"     
> >
> >other attached packages:
> >AnnBuilder    RSQLite        DBI   annotate       
> XML
> >   Biobase 
> >  "1.10.2"    "0.4-1"   "0.1-10"   "1.10.0"  
> "0.99-7"
> >  "1.10.0" 
> >>
> >
> >
> >--- nli at fhcrc.org wrote:
> >
> >> Sorry, the OS X version of AnnBuilder v1.10.2 is
> not
> >> available yet. We will try
> >> to get it ready as soon as possible.
> Alternatively,
> >> you can download the source
> >> from
> >>
>
>http://www.bioconductor.org/packages/bioc/1.8/html/AnnBuilder.html
> >> and
> >> install it yourself. The modification that
> matters
> >> to you is in
> >> AnnBuilder/R/GP.R . 
> >> 
> >> best
> >> 
> >> nianhua
> >> 
> >> Quoting Luo Weijun <luo_weijun at yahoo.com>:
> >> 
> >> > Thank you so much, Nianhua,
> >> > I think it works now. One more question, You
> >> suggested
> >> > me to update AnnBuilder to the lastest version,
> >> > 1.10.1, since The UCSC Genome 
> >> > database has updated. But I am not sure exactly
> >> how to
> >> > do it. I tried to update AnnBuilder package
> with
> >> > biocLite('AnnBuilder'), as well as using
> >> > update.packages(repos=biocReposList())
> following
> >> > Seth¡¯s suggestion, all I got is still the old
> >> > version, AnnBuilder_1.10.0. Therefore, could
> you
> >> tell
> >> > me how can I update to the lastest AnnBuilder
> >> version?
> >> > 
> >> > This is my session info after
> >> > update.packages(repos=biocReposList())
> >> > 
> >> > > sessionInfo()
> >> > Version 2.3.1 (2006-06-01) 
> >> > powerpc-apple-darwin8.6.0 
> >> > 
> >> > attached base packages:
> >> > [1] "tools"     "methods"   "stats"    
> "graphics"
> >> 
> >> > "grDevices" "utils"    
> >> > [7] "datasets"  "base"     
> >> > 
> >> > other attached packages:
> >> > AnnBuilder    RSQLite        DBI   annotate    
>   
> >> XML
> >> >    Biobase 
> >> >   "1.10.0"    "0.4-1"   "0.1-10"   "1.10.0"  
> >> "0.99-7"
> >> >   "1.10.0" 
> >> > >
> >> > I really appreciate your help!
> >> > Weijun
> >> > 
> >> > 
> >> >
> __________________________________________________
> >> > Do You Yahoo!?
> >
> >> protection around 
> >> > http://mail.yahoo.com 
> >> > 
> >> 
> >> 
> >> 
> >> 
> >>
> >
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> 
> Jianhua Zhang
> Department of Medical Oncology
> Dana-Farber Cancer Institute
> 44 Binney Street
> Boston, MA 02115-6084
> 
>