Hi P.Terry,

Thanks to both Wolfgang and Steffen for explaining the database situation! In stead of chasing down each duplicate entries in different databases, I decided to output one entry for each exon ID, and output a warning message alerting the users the list of exon ids with duplicated entries. This way the users who are the expert of the queried database, can choose to resolve the duplicated entries with the list of ids.

The fix is in dev 1.3.11.

Best regards,

Julie


*******************************************
Lihua Julie Zhu, Ph.D
Research Associate Professor
Program Gene Function and Expression
University of Massachusetts Medical School
364 Plantation Street, Room 613
Worcester, MA 01605
508-856-5256
http://www.umassmed.edu/pgfe/faculty/zhu.cfm
*******************************************


On 3/5/10 6:46 PM, "pterry@huskers.unl.edu" <pterry@huskers.unl.edu> wrote:

 Dear bioc-sig-sequencing,

I would like to annotate chip-seq peaks for the arabidopsis genome.  "TSS" and "Exon" are two of the arguments for the 'getAnnotation' function.  The "TSS" argument succeeded, but the "Exon" argument failed.

...
> arabdset<-useMart(biomart="plant_mart_4", dataset = "athaliana_eg_gene")
Checking attributes ... ok
Checking filters ... ok
> ExonArabAnno<-getAnnotation(arabdset, featureType="Exon")
Error in `rownames<-`(`*tmp*`, value = c("ATCG00010.1-E176369", "ATMG00010.1-E176520",  :
  duplicate rownames not allowed

> sessionInfo()
R version 2.11.0 Under development (unstable) (2010-02-28 r51186)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] ChIPpeakAnno_1.3.4                  org.Hs.eg.db_2.3.6
 [3] GO.db_2.3.5                         RSQLite_0.8-3
 [5] DBI_0.2-5                           AnnotationDbi_1.9.4
 [7] BSgenome.Ecoli.NCBI.20080805_1.3.16 BSgenome_1.15.11
 [9] Biostrings_2.15.22                  IRanges_1.5.51
[11] multtest_2.3.0                      Biobase_2.7.4
[13] biomaRt_2.3.4

loaded via a namespace (and not attached):
[1] MASS_7.3-5      RCurl_1.3-1     splines_2.11.0  survival_2.35-8
[5] tools_2.11.0    XML_2.6-0
>

Can someone comment?


Thanks,
P. Terry
pterry@huskers.unl.edu

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