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

[Luo Weijun]

Hello Nianhua,
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: 

> 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/hs95av2Entrezg7Base.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 
> > 
> 
> 
> 
> 
>