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

[Luo Weijun]

Thanks a lot, 
I will wait till tomorrow to get the source code from
bioconductor website, since the website at
https://hedgehog.fhcrc.org/ needs account/password.
And I agree there may be some backward compatibility
issues between AnnBuilder 1.11.x and R 2.3.x. (I will
try it out tomorrow.) In that case, I can only use
AnnBuilder 1.10.x currently and in the near future,
since R 2.4.x is not released yet. Therefore, I am
looking forward to your results in checking AnnBuilder
1.10.x. Please keep me posted. Thanks.
Weijun

--- nli at fhcrc.org wrote:

> 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
> > >> >>
> 
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