[BioC] Using biomaRt to check probe locations

Nathan Harmston iwanttobeabadger at googlemail.com
Mon Aug 11 14:50:52 CEST 2008


I have just found a few of the probes which I find to be significantly
diff expression in one of my analysis, have no attached genomic
location in the annotation package I am using. So I thought a way
around this would be to query ensembl using biomaRt and retrieve
probe_set locations from ensembl (since I trust Ensembl infinitely
more than Affy), however in the listAttributes(ensembl) I have been
unable to determine the attribute that I require to determine the
start and end location and strand of the actual probe involved,
however all I can get back are transcript locations and gene

For example probe: 1552422_at from the hgu133plus2 array.

Is there an attribute that I am missing that can be used?

Also just out of interest, does getBM have the 3 second break
automatically or not? or does it use one big query? I ve only been
using 1 test probe, and would like to make sure I am not going to get
myself and my university blocked.

Many thanks in advance,


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