Dear list,

I am trying to build an Annotation package for the hgu133plus2 array (Affy
array, human). For my data analysis I have been using the remapped
hs133phsentrezgcdf package. An annotation package exists for this CDF but
the contained information is very limited. So I decided to build  my own,
using AnnBuilder.
Here's the code I used:

#####
  library(AnnBuilder)
  library(hs133phsentrezgcdf)
  fN <- ls(hs133phsentrezgcdf)   # to extract the featureNames in this CDF
  cfN <- sub("_at", "", fN)     #  to obtain the entrez gene IDs

## construct the base file
  mygeneNMap <- matrix(c(fN, cfN), byrow=F, ncol =2)
  write.table(mygeneNMap, file = "geneNMap", sep = "\t", quote = FALSE,
row.names = FALSE, col.names = FALSE)

## retrieve where to go look for the info
mySrcUrls <- getSrcUrl("all", "Homo sapiens")

myDir <- "."

  mySrcUrls <- getSrcUrl("all", "Homo sapiens")

 ABPkgBuilder(baseName = "geneNMap", srcUrls = mySrcUrls,
   baseMapType  = "ll", pkgName = "hs133phsentrezgannot",
   pkgPath = ".", organism =  "Homo sapiens", version = "1.1.0",
   author = list(authors = "Tine Casneuf",  maintainer =
   "Tine, <tineke.casneuf@gmail.com"), fromWeb = TRUE)
######

My baseName file has the probeset IDs in the first column, the Entrez Gene
ID in the second and thus looks like this:
 > read.table(file = "geneNMap", sep ="\t")[1:4,]
        V1   V2
 1    1_at    1
 2   10_at   10
 3  100_at  100
 4 1000_at 1000

The  ABPkgBuilder function runs without errors or significant warnings. The
package build and can be installed but no mapping could be done for my data,
as you can see below:

> hs133phsentrezgannot()

Quality control information for  hs133phsentrezgannot
Date built: Created: Thu Jan 10 11:55:27 2008

Number of probes: 17589
Probe number missmatch: None
Probe missmatch: None
Mappings found for probe based rda files:
         hs133phsentrezgannotCHRLOC found 0 of 17589
         hs133phsentrezgannotENTREZID found 0 of 17589
         hs133phsentrezgannotENZYME found 0 of 17589
         hs133phsentrezgannotPATH found 0 of 17589
Mappings found for non-probe based rda files:
         hs133phsentrezgannotCHRLENGTHS found 25
         hs133phsentrezgannotORGANISM found 1
         hs133phsentrezgannotPFAM found 0
         hs133phsentrezgannotPROSITE found 0
Does anyone have a clue what I am doing wrong? It will probably be something
small, but I cannot figure it out.

Many thanks in advance!
Best,
Tine

#####
My sessionInfo:
> sessionInfo()
R version 2.6.1 (2007-11-26)
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] hs133phsentrezgannot_1.1.0  GO_2.0.1
hs133phsentrezgprobe_10.0.0 matchprobes_1.10.0
 [5] hs133phsentrezgcdf_10.0.0   AnnBuilder_1.16.0
annotate_1.16.1             xtable_1.5-2
 [9] AnnotationDbi_1.0.6         RSQLite_0.6-4
DBI_0.2-4                   XML_1.93-2.1
[13] affy_1.16.0                 preprocessCore_1.0.0
affyio_1.6.1                Biobase_1.16.2
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17
>

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