[BioC] AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)
jzhang at jimmy.harvard.edu
Thu Jul 13 20:05:06 CEST 2006
>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
>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
> 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.
>Version 2.3.1 (2006-06-01)
>attached base packages:
> "tools" "methods" "stats" "graphics"
> "datasets" "base"
>other attached packages:
>AnnBuilder RSQLite DBI annotate XML
> "1.10.2" "0.4-1" "0.1-10" "1.10.0" "0.99-7"
>--- 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
>> install it yourself. The modification that matters
>> to you is in
>> AnnBuilder/R/GP.R .
>> Quoting Luo Weijun <luo_weijun at yahoo.com>:
>> > Thank you so much, Nianhua,
>> > I think it works now. One more question, You
>> > 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
>> > me how can I update to the lastest AnnBuilder
>> > 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:
>> >  "tools" "methods" "stats" "graphics"
>> > "grDevices" "utils"
>> >  "datasets" "base"
>> > other attached packages:
>> > AnnBuilder RSQLite DBI annotate
>> > Biobase
>> > "1.10.0" "0.4-1" "0.1-10" "1.10.0"
>> > "1.10.0"
>> > >
>> > I really appreciate your help!
>> > Weijun
>> > __________________________________________________
>> > Do You Yahoo!?
>> protection around
>> > http://mail.yahoo.com
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