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

[Luo Weijun]

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.
(please all see below for more details)

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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