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

[John Zhang]

>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