[BioC] Interface to BASE microarray data

Henrik Bengtsson hb at maths.lth.se
Sun Jul 16 13:30:31 CEST 2006

On 7/14/06, Daniel Brewer <daniel.brewer at icr.ac.uk> wrote:
> Hi,
> Is there any bioconductor packages to allow the extraction of data from
> the BASE microarray database (http://base.thep.lu.se/) within R.  There
> seems to be some plugins to allow one to perform microarray analysis
> using R within BASE,

That is the aroma.Base package (http://www.braju.com/R/) and it is
compatible with BASE v1.2; The upcoming BASE v2 is totally different,
although they plan to be backward compatible with v1.2 plugins.

> but nothing about how to get data when within R.  I
> know this is possible from within GeneSpring (with the appropriate
> plugin), so I thought there might be a way to do it from within R.

The aroma.Base package has classes to communicate data with BASE v1.2
to plugins, which is done via stdout/stdin.  However, the package has
*no* code for interaction with the BASE database, but you should be
able to use SQL from R to access the database.  BUT BUT BUT, I'm not
sure if you're really supposed to do this with BASE v1.2 - you have to
check with the BASE people about this.

In BASE v2 there is/will be a database API, which will be implemented
in Java and I guess you could setup the same API in R.   Check BASE
devel for more details.  I have no immediate plans to implement BASE
v2 in aroma.Base (because my priorities are elsewhere right now).



> Many Thanks
> Daniel Brewer
> --
> **************************************************************
> Daniel Brewer, Ph.D.
> Institute of Cancer Research
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