Dear list,

it looks like there may be a bug in function 'getBM' affecting the use of
attribute 'validated':

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>library(biomaRt)
>mart = useMart("ensembl")
>ensembl = useDataset("hsapiens_gene_ensembl", mart = mart);

>library(hgu133plus2.db);
>EID <- toTable(hgu133plus2ENTREZID);
>I <- sample(dim(EID)[1],100)
>p <- EID[I,"probe_id"];
> head(p)
[1] "205953_at"   "214718_at"   "233633_at"   "241572_at"   "224704_at"
[6] "221510_s_at"


>Q <-
getBM(attributes=c("affy_hg_u133_plus_2","entrezgene","validated"),filters="affy_hg_u133_plus_2",mart=ensembl,values=p);

                                                                          V1
1 Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple
attribute pages are not allowed
Errore in getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene",
"validated"),  :
  Number of columns in the query result doesn't equal number of attributes
in query.  This is probably an internal error, please report.


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The above error message disappears when running the same query after having
removed "validated" from the list of attributes.
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>Q <-
getBM(attributes=c("affy_hg_u133_plus_2","entrezgene"),filters="affy_hg_u133_plus_2",mart=ensembl,values=p);
>head(Q)
  affy_hg_u133_plus_2 entrezgene
1        1552538_a_at         NA
2        1552538_a_at     221458
3        1554485_s_at     140738
4        1555097_a_at       5737
5          1564015_at         NA
6        1564198_a_at     118611


>sessionInfo()
 R version 2.8.1 (2008-12-22)
 i486-pc-linux-gnu

 locale:
 LC_CTYPE=it_IT.UTF-8;LC_NUMERIC=C;LC_TIME=it_IT.UTF-8;LC_COLLATE=it_IT.UTF-8;LC_MONETARY=C;LC_MESSAGES=it_IT.UTF-8;LC_PAPER=it_IT.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=it_IT.UTF-8;LC_IDENTIFICATION=C

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

 other attached packages:
 [1] hgu133plus2.db_2.2.5 RSQLite_0.7-1        DBI_0.2-4
  [4] AnnotationDbi_1.4.3  Biobase_2.2.2        biomaRt_1.16.0

 loaded via a namespace (and not attached):
 [1] RCurl_0.94-1 XML_2.1-0
--------------------------------------------------------------------------------------------------------------------


Best wishes
teresa
____________________________
Teresa Colombo, PhD Student
Prof G. Macino Lab
Dept of Cellular Biotechnology and Hematology
'Sapienza' University of Rome
Phone/Fax: +39 06 4457731

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