[BioC] Converting an Annbuilder object to a dataframe

[Sean Davis]

On Monday 08 January 2007 07:17, Daniel Brewer wrote:
> Sean Davis wrote:
> > On Friday 05 January 2007 10:51, Daniel Brewer wrote:
> >> We are trying to use data from arrays that were hybed using tumour DNA
> >> for CGH purposes.
> >
> > Since you are working with cDNAs, you might want to map them directly
> > using UCSC which aligns ESTs and mRNAs directly to the genome.  This is
> > subtly different from mapping the cDNAs to genes and then mapping those
> > genes to the genome, which is what is done by AnnBuilder.  You can use
> > the UCSC table browser to find the locations of your clones of interest.
> >
> > Sean
>
> That sounds like a good idea, but unfortunately it does not appear that
> UCSC has any knowledge of Agilent 4100a probes.  Been searching around
> to try and get the equivalent information or either the sequence, but
> without luck.

If the probes were cDNAs, then you likely have Genbank accession numbers.  
That is what you would use for the location.

Sean