[BioC] AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)
nli at fhcrc.org
nli at fhcrc.org
Thu Jul 13 22:41:50 CEST 2006
Hi,
It seems we have some problems here. Let me clarify things first:
1. There are two svn source repositories: the bioconductor 1.8 release
repository where AnnBuilder 1.10.x belong to and the devel repository where
AnnBuilder 1.11.x belong to. John fixed the problem of AnnBuilder at the devel
repository today and the latest version is 1.11.4. You can get the code from
our svn repository at
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnBuilder now, or
you can get it from
http://www.bioconductor.org/packages/1.9/bioc/html/AnnBuilder.html TOMORROW.
The corresponding OS X binary will be ready after a week.
2. The packages in devel repository (including AnnBuilder 1.11.x) are for R
2.4.x. Therefore, they may not be backward compatiable with R 2.3.x. Please give
it a try. I am not able to test it in my current setting. Sorry.
3. I thought AnnBuilder 1.10.x should work the same as 1.11.x, so I used 1.11.x
for testing but referred to 1.10.x in my previous replies. But I was wrong,
sorry. I tested both AnnBuilder 1.11.2 (3 column baseFile) and AnnBuilder
1.11.4 by using your exact baseFile, and both worked fine. I test AnnBuilder
1.10.x just now, but it didn't work. I need more time to look into it.
I will update you later... Please try either AnnBuiler 1.11.2 or 1.11.4 for now.
Sorry for the inconvenience.
nianhua
Quoting John Zhang <jzhang at jimmy.harvard.edu>:
>
> >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
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >
> >> >_______________________________________________
> >> >Bioconductor mailing list
> >> >Bioconductor at stat.math.ethz.ch
> >> >https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> >Search the archives:
> >>
> >http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >> Jianhua Zhang
> >> Department of Medical Oncology
> >> Dana-Farber Cancer Institute
> >> 44 Binney Street
> >> Boston, MA 02115-6084
> >>
> >>
> >
> >
> >__________________________________________________
> >Do You Yahoo!?
> >Tired of spam? Yahoo! Mail has the best spam protection around
> >http://mail.yahoo.com
>
> Jianhua Zhang
> Department of Medical Oncology
> Dana-Farber Cancer Institute
> 44 Binney Street
> Boston, MA 02115-6084
>
>
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