NA values in Biomart query

Hi, =

I want to retrieve some annotation informations from "ensembl exon id" by u=
sing a biomart query : "ensembl gene id", "ensembl transcript id", ...
After my "getBM" query, without error message, my object "results" contains=
 lot of "NA" values but if I re-send a query on "NA" values id, I successfu=
lly retrieve informations.

Example : =

library(biomaRt)
ensembl <-  useMart(host=3D"jan2013.archive.ensembl.org", biomart=3D"ENSEMB=
L_MART_ENSEMBL", dataset =3D "hsapiens_gene_ensembl")

results <- getBM(attributes=3Dc("ensembl_exon_id","ensembl_gene_id"),filter=
s=3D"ensembl_exon_id",values=3DENSE,mart=3Densembl, uniqueRows=3DTRUE)
My object ENSE contain 512120 exon_id.

Why I obtain lot of "NA" values when my value option  is large ? Must I to =
split it ? and Why ? =


Thanks, =


Elodie

sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=3Dfr_FR.UTF-8       LC_NUMERIC=3DC              =

 [3] LC_TIME=3Dfr_FR.UTF-8        LC_COLLATE=3Dfr_FR.UTF-8    =

 [5] LC_MONETARY=3Dfr_FR.UTF-8    LC_MESSAGES=3Dfr_FR.UTF-8   =

 [7] LC_PAPER=3Dfr_FR.UTF-8       LC_NAME=3DC                 =

 [9] LC_ADDRESS=3DC               LC_TELEPHONE=3DC            =

[11] LC_MEASUREMENT=3Dfr_FR.UTF-8 LC_IDENTIFICATION=3DC       =


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


other attached packages:
[1] biomaRt_2.20.0

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.26.0 Biobase_2.24.0       BiocGenerics_0.10.0 =

 [4] DBI_0.2-7            GenomeInfoDb_1.0.2   IRanges_1.22.9      =

 [7] parallel_3.1.1       RCurl_1.95-4.1       RSQLite_0.11.4      =

[10] stats4_3.1.1         tools_3.1.1          XML_3.98-1.1  =





Elodie Chapeaublanc
IE Bioinformatique
=C9quipe Oncologie Mol=E9culaire
Institut Curie - UMR 144 - CNRS
26 rue d'Ulm - 75248 Paris Cedex 05
Tel: +33 1 56 24 63 57
Email: [email protected]
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