[BioC] Re : "Testing" the connection of getBM() ?

Caroline caroline.johnston at iop.kcl.ac.uk
Fri Apr 17 16:36:13 CEST 2009


> I'm not sure I understand the "vectorized queries". Actually, I submit vectors too in my getBM() command....

I thought I understood this and now I think I don't - can someone
clarify for me? 

I was under the impression that if I used a filter then the results I
got back would be those for which *any* of the values of that filter
were true. eg. using ensembl_gene_id and affy_hg_u133_plus_2 with values
list(c(ensid_1, ensid_2), c(affyid_1, affyid_2)) then the results I'd
get back would have either of the affy IDs and either of the ensembl IDs
- the values aren't paired - a gene with ensid_1 and affyid_2 is a valid

I know Biomart interprets the combination of filters chromosome_name,
start and end as a range filter, but I'm not sure what it means to have
multiple values for start and end - elements falling within any of the
start or end values?. A quick test suggests that it returns anything
falling between the smallest start and largest end position. So, how do
you vectorize a range filter? I've looked at both the Vignette and the
getBM docs and am none the wiser.



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