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

[Luo Weijun]

Hello All,
I posted this a couple of days ago, following some
nice feedback. But haven't got further response yet,
could anybody give me any suggestion/ideas on this
problem? Thank you so much.
Weijun



--- Luo Weijun <luo_weijun at yahoo.com> wrote:

Thank you so much, guys, 
For John's question, My base map type is "ll", since
my probes are mapped to Entrez Gene IDs directly. 
For Nianhua's question, below is all my codes for this
work.  

library(AnnBuilder)
load('/Users/luow/project/microarraydata/annotation/hs95av2Entrezg7.Rdata')
myBase=cbind(hs95av2Entrezg7,hs95av2Entrezg7)
myBase[,1]=paste(hs95av2Entrezg7,'_at',sep='')
write.table(myBase,file='/Users/luow/project/microarraydata/annotation/hs95av2Entrezg7Base.txt',sep='\t',row.names=F,col.names=F)
myBase='/Users/luow/project/microarraydata/annotation/hs95av2Entrezg7Base.txt'
myBaseType <- "ll"

myDir <-
'/Users/luow/project/microarraydata/annotation/'
ABPkgBuilder(baseName = myBase, baseMapType =
myBaseType,
pkgName = "hs95av2Entrezg7", pkgPath = myDir,
organism = "Homo sapiens", version = "1.1.0", author =
list(authors = "Weijun",
maintainer = "Weijun <luo_weijun at yahoo.com>"), fromWeb
=T)


Here is part of my base file:
>
a=read.delim('/Users/luow/project/microarraydata/annotation/hs95av2Entrezg7Base.txt',sep='\t',
head=F)
> head(a)                                             
                                                 
        V1    V2
1 10001_at 10001
2 10002_at 10002
3 10003_at 10003
4 10004_at 10004
5 10005_at 10005
6 10006_at 10006

Here is what I got when I created and installed the
package. And Nianhua is right, I got problem with
hs95av2Entrezg7CHRLOC environment, no entry at all. I
will need to update my AnnBuilder. But exactly how can
I do that, using update.packages function or, is there
anything for updating bioc packages specially?

> library(hs95av2Entrezg7)
> hs95av2Entrezg7()


Quality control information for  hs95av2Entrezg7 
Date built: Created: Sat Jul  8 20:23:41 2006  
 
Number of probes: 8359 
Probe number missmatch: None 
Probe missmatch: None 
Mappings found for probe based rda files: 
         hs95av2Entrezg7CHRLOC found 0 of 8359
         hs95av2Entrezg7ENZYME found 1313 of 8359
         hs95av2Entrezg7LOCUSID found 8292 of 8359
         hs95av2Entrezg7PATH found 2784 of 8359 
Mappings found for non-probe based rda files:
         hs95av2Entrezg7CHRLENGTHS found 25
         hs95av2Entrezg7ENZYME2PROBE found 651
         hs95av2Entrezg7ORGANISM found 1
         hs95av2Entrezg7PATH2PROBE found 180
         hs95av2Entrezg7PFAM found 6997
         hs95av2Entrezg7PROSITE found 5451 

Please let me know if you have any ideas, suggestions,
or other questions. I really appreciate all the kind
help you guys offer!
Weijun


> 
> 
> --- Nianhua Li <nli at fhcrc.org> wrote:
> 
> > Hi, Weijun,
> > 
> > The humanLLMappings package was generated by
> > function map2LL rather than 
> > ABPkgBuilder, therefore it is a different case. I
> > used ABPkgBuilder 
> > function generate a coupld of pakcages recently,
> and
> > didn't see 
> > xxGENENAME or xxSYMBOL environments have any
> > problem. So, I suspect the 
> > problem is specific to your input data. Could you
> > please provide more 
> > details? e.g. myBaseType and maybe also a small
> part
> > of myBase
> > Also, you may want to upgrade AnnBuilder to
> 1.10.1.
> > The UCSC Genome 
> > database updated their schema (one table) recently
> > for human and mouse 
> > data, and AnnBuilder has been updated
> > correspondingly. If you see 
> > problems with xxCHRLOC environment, please update
> > your AnnBuilder.
> > 
> > thanks
> > 
> > nianhua
> > 
> > Nianhua Li
> > Computational Biology, PHS, FHCRC
> > 
> > _______________________________________________
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> >
> 
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