[BioC] reducing gene number in affybatch objects
Hinnerk Boriss
boriss at izbi.uni-leipzig.de
Wed May 28 16:14:46 MEST 2003
> > for teaching purposes I would like to cut down the number
> of genes in
> > affybatch objects so that students won't have to wait that long for
> > their computations. Unfortunately, I cannot figure out how
> to do that.
> > Any hints? Thanks!
>
> Cutting down the size of an AffyBatch is not straightforward (for the
> moment, it should be in the future). There are implications if one
> does so (think about the spatial background correction as done
> in mas 5.0). I believe that the "slowest" part is the computation of
> summary expression values. You may want to investigate the use of the
> parameter 'ids' for the method 'computeExprSet'
> (or 'summary.subset' for the function 'expresso',
> you can ask for the summary of a given set of affyids).
I've played with this, but it doesn't really help much because the
student's computers are a bit on the slow end.
How was the affybatch.example object created from the Lemon data? If its
not too painful, I could try this approach.
Best,
Hinnerk
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