[BioC] Help using biomaRt

john seers (IFR) john.seers at bbsrc.ac.uk
Fri Jan 23 17:00:17 CET 2009


Hi All 

I am just learning to use biomaRt from R and could do with a little help
please. I have worked my way through the user guide and "How to build a
biomaRt" query and that has all worked fine. But now I am trying to
build my own queries and have a couple of questions.  

Question 1

I am using the Ensembl database. Looking at the www.ensembl.org website
it looks like you do not have to specify a filter. Do you have to
specify a filter using biomaRt/R? If not how is it done?

Question 2

While trying things I get the following error message, presumably caused
by the attribute not being in that table.  

1 Query ERROR: caught BioMart::Exception::Usage: Attributes from
multiple attribute pages are not allowed
Error in getBM(attnames, filters = filtnames, values = transcripts, mart
= mart) : 
  Number of columns in the query result doesn't equal number of
attributes in query.  This is probably an internal error, please report.

How can I avoid this error other than by trial and error? Is there a bit
more documentation somewhere that I have not found that describes the
data structure/format in more detail? i.e. how to select the attributes
that are not on "multiple attribute pages"?  At the moment I am just
building my queries by trying something and seeing if it works which
does not seem right. I think there must be some more information that
will make it a bit easier.

Also I cannot find anything that describes the groups/categories/types
and what they mean or do.

Thank you for any help.





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