[BioC] BioMaRt query

[James W. MacDonald]

Hi Rene,

On 10/4/2010 4:44 AM, René Dreos wrote:
> 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?

Because you are querying two different data sources and have found an 
instance in which they are not consistent. This is a pretty common 
occurrence, given how fluid gene definitions are (and likely will be for 
some time).

Best,

Jim


>
> 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
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues