HI, Nianhua:

I am using annotationDBI and it is much better than AnnBuilder ( I used to
use that package).
I found the package I built recently with annotationDBI has ACCNUM match
zero. Here is what I did:

1. My code:
  source("http://bioconductor.org/biocLite.R")
  biocLite("mouse.db0")


  makeMOUSECHIP_DB(affy=FALSE,
  prefix="Rosetta",
  fileName='Rosettabasefile.txt',
  baseMapType="eg",
  outputDir = getwd(),
  version="3.0.0",
  manufacturer = "Rosetta",
  chipName = "Mouse custom Array",
  manufacturerUrl = "http://www.rii.com/")

2. My base file (example):
   10024408304           NA  10024412833 78124  10024395853 50766
10024401691 327766  10024407521        NA  10024397162 192651  10024402992
216395  10024414142 69334  10024410918 105203  10024410918 105203
10024416230 19159  10024416583 22312 I noticed that I have duplicates in
both column.

3. the information I got:

4. Can you notice that I have RosettaACCNUM match zero? how does this
happen?

Thanks

Shiliang


R version 2.7.2 (2008-08-25)
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> library(Rosetta.db)
Loading required package: AnnotationDbi
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: DBI
Loading required package: RSQLite
> Rosetta()
Quality control information for Rosetta:


This package has the following mappings:

RosettaACCNUM has 0 mapped keys (of 23574 keys)
RosettaALIAS2PROBE has 65400 mapped keys (of 65400 keys)
RosettaCHR has 19189 mapped keys (of 23574 keys)
RosettaCHRLENGTHS has 21 mapped keys (of 21 keys)
RosettaCHRLOC has 17558 mapped keys (of 23574 keys)
RosettaENSEMBL has 18414 mapped keys (of 23574 keys)
RosettaENSEMBL2PROBE has 17096 mapped keys (of 17096 keys)
RosettaENTREZID has 19207 mapped keys (of 23574 keys)
RosettaENZYME has 1922 mapped keys (of 23574 keys)
RosettaENZYME2PROBE has 791 mapped keys (of 791 keys)
RosettaGENENAME has 19207 mapped keys (of 23574 keys)
RosettaGO has 16380 mapped keys (of 23574 keys)
RosettaGO2ALLPROBES has 8447 mapped keys (of 8447 keys)
RosettaGO2PROBE has 6152 mapped keys (of 6152 keys)
RosettaMAP has 18233 mapped keys (of 23574 keys)
RosettaMGI has 19053 mapped keys (of 23574 keys)
RosettaMGI2PROBE has 17459 mapped keys (of 17459 keys)
RosettaPATH has 4072 mapped keys (of 23574 keys)
RosettaPATH2PROBE has 195 mapped keys (of 195 keys)
RosettaPFAM has 18761 mapped keys (of 23574 keys)
RosettaPMID has 19063 mapped keys (of 23574 keys)
RosettaPMID2PROBE has 114988 mapped keys (of 114988 keys)
RosettaPROSITE has 18761 mapped keys (of 23574 keys)
RosettaREFSEQ has 18781 mapped keys (of 23574 keys)
RosettaSYMBOL has 19207 mapped keys (of 23574 keys)
RosettaUNIGENE has 18950 mapped keys (of 23574 keys)


Additional Information about this package:

DB schema: MOUSECHIP_DB
DB schema version: 1.0
Organism: Mus musculus
Date for NCBI data: 2008-Apr2
Date for GO data: 200803
Date for KEGG data: 2008-Apr1
Date for Golden Path data: 2007-Aug22
Date for IPI data: 2008-Mar19
> sessionInfo()
R version 2.7.2 (2008-08-25)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
base

other attached packages:
[1] Rosetta.db_3.0.0    AnnotationDbi_1.2.2 RSQLite_0.7-0
DBI_0.2-4           Biobase_2.0.1
>

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