[BioC] AnnBuilder problem with CHR slot

[Dario Greco]

dear all,

i am trying to build up an annotation package for a cDNA custom platform
using ABPkgBuilder() based on EntrezGene IDs.
the problem is that no probe is mapped in the "CHR" slot.

my base file is (first 20 rows of 32447):
 1_spt	22932
 10_spt	5575
 100_spt	2260
 1000_spt	124540
 10000_spt	23768
 10001_spt	5288
 10002_spt	434
 10003_spt	586
 10004_spt	26221
 10005_spt	5551
 10006_spt	909
 10007_spt	10817
 10008_spt	4004
 10009_spt	NA  
 1001_spt	57484
 10010_spt	202
 10011_spt	NA  
 10012_spt	538
 10013_spt	2050
 10014_spt	1360

my URLs are:
x<-getSrcUrl("all", organism="Homo sapiens")

my QC output is:
E5annEGQC
[1] "\n\nQuality control information for  E5annEG \nDate built: Created: Fri
Aug
4 11:47:40 2006  \n \nNumber of probes: 32448 \nProbe number missmatch: None
\
nProbe missmatch: None \nMappings found for probe based rda files: \n\t
E5annEGA
CCNUM found 0 of 32448\n\t E5annEGCHRLOC found 27954 of 32448\n\t E5annEGCHR
fou
nd 0 of 32448\n\t E5annEGENZYME found 3740 of 32448\n\t E5annEGGENENAME found
0
of 32448\n\t E5annEGLOCUSID found 29426 of 32448\n\t E5annEGMAP found 0 of
32448
\n\t E5annEGOMIM found 0 of 32448\n\t E5annEGPATH found 7620 of 32448\n\t
E5annE
GPMID found 0 of 32448\n\t E5annEGREFSEQ found 0 of 32448\n\t E5annEGSYMBOL
foun
d 0 of 32448\n\t E5annEGUNIGENE found 0 of 32448 \nMappings found for
non-probe
based rda files:\n \t E5annEGCHRLENGTHS found 25\n\t E5annEGENZYME2PROBE found
6
24\n\t E5annEGORGANISM found 1\n\t E5annEGPATH2PROBE found 178\n\t E5annEGPFAM
f
ound 22380\n\t E5annEGPROSITE found 15130 \n\n"


sessionInfo():
attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "base"
other attached packages:
         GO AnnBuilder    RSQLite        DBI   annotate        XML    Biobase
   "1.10.0"   "1.11.4"    "0.4-1"   "0.1-10"   "1.10.0"   "0.99-7"   "1.10.0"


do you have any suggestion?
thanks for your help!
sincerely
Dario

-- 

Dario Greco

Institute of Biotechnology - University of Helsinki
Building Cultivator II
P.O.Box 56	Viikinkaari 4
FIN-00014	Finland

Office: +358 9 191 58951
Fax: +358 9 191 58952
Mobile: +358 44 023 5780

Lab WebPage: http://www.biocenter.helsinki.fi/bi/dna-microarray/
Personal WebPage: http://www.biocenter.helsinki.fi/bi/dna-
microarray/dario.htm