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

Luo Weijun luo_weijun at yahoo.com
Wed Jul 12 18:26:02 CEST 2006

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.
BTW, I tried to update AnnBuilder package with
biocLite('AnnBuilder') all I got is still the old
version, AnnBuilder_1.10.0, I am not sure exactly how
to get the updated version AnnBuilder_1.10.1, as
suggested by Nianhua in an earlier message. 

##older messages###
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.  

myBaseType <- "ll"

myDir <-
ABPkgBuilder(baseName = myBase, baseMapType =
pkgName = "hs95av2Entrezg7", pkgPath = myDir,
organism = "Homo sapiens", version = "1.1.0", author =
list(authors = "Weijun",
maintainer = "Weijun <luo_weijun at yahoo.com>"), fromWeb

Here is part of my base file:
> 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!

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