Dear BioC mailing list,

I am trying to annotate Arabidopsis ATH1 genome array results using biomaRt,
but it looks like some of the probesets are not annotated in biomaRt
database. Here is one example:

> library(biomaRt)
> AT.db <- useMart(biomart="plant_mart_6", dataset="athaliana_eg_gene")
> getBM(attributes = c("affy_ath1_121501","ensembl_gene_id","description"),
filters = "affy_ath1_121501", values = "254998_at", mart = AT.db)
[1] affy_ath1_121501 ensembl_gene_id  description
<0 rows> (or 0-length row.names)

But if I use ath1121501.db library to annotate the same probeset:

> library(annotate)
> library(ath1121501.db)

> mget("254998_at", env=ath1121501GENENAME)
$`254998_at`
[1] "encodes a choline synthase whose gene expression is induced by high
salt and mannitol."

> mget("254998_at", env=ath1121501ACCNUM)
$`254998_at`
[1] "AT4G09760"

Why is this happening?

Thank you for any advice,
best regards
r

> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-apple-darwin9.8.0

locale:
[1] C

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

other attached packages:
 [1] ath1121501.db_2.4.1       org.At.tair.db_2.4.3
 [3] RSQLite_0.9-2             annotate_1.26.1
 [5] ath1121501cdf_2.6.0       biomaRt_2.4.0
 [7] genefilter_1.30.0         marray_1.26.0
 [9] gplots_2.8.0              caTools_1.10
[11] bitops_1.0-4.1            gdata_2.7.2
[13] gtools_2.6.2              bradiar1b520742cdf_1.24.0
[15] arrayQualityMetrics_2.6.0 affyPLM_1.24.1
[17] gcrma_2.20.0              preprocessCore_1.10.0
[19] matchprobes_1.20.0        Biostrings_2.16.9
[21] IRanges_1.6.15            AnnotationDbi_1.10.2
[23] affxparser_1.20.0         makecdfenv_1.26.0
[25] lattice_0.18-8            RMySQL_0.7-5
[27] DBI_0.2-5                 affy_1.26.1
[29] Biobase_2.8.0             limma_3.4.4

loaded via a namespace (and not attached):
 [1] RColorBrewer_1.0-2  RCurl_1.4-2         XML_3.1-1
 [4] affyio_1.16.0       beadarray_1.16.0    hwriter_1.2
 [7] latticeExtra_0.6-14 simpleaffy_2.24.0   splines_2.11.1
[10] stats4_2.11.1       survival_2.35-8     tools_2.11.1
[13] vsn_3.16.0          xtable_1.5-6

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