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

[John Zhang]

>Thank you, John. Shall I use 2-column or 3-column base

Two columns.

>file for the new version of AnnBuilder? And the new

The version I checked in is 1.11.4. I am not sure when the new version will be 
pushed. Nianhua knows better.


>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/hs95av2Entrezg7Ba
s
>> 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
>> 
>> 
>
>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084