[BioC] justGCRMA normalisation options?

[Rafael A. Irizarry]

justGCRMA is already in the unstable devel version. 

the internal function gcrma.engine permits you to do just background 
correction. you can then use expresso to choose whatever other 
option you want. its not easy to use so we will look into 
creating an easy to use wrapper for it.





On Fri, 19 Mar 2004, Andrew Harrison wrote:

> Hi,
> 
> 	Firstly, GCRMA rocks and many thanks to all those 
> involved in producing it. 
> 
> 	However, GCRMA is painfully slow. I understand there are plans 
> for a justGCRMA. Will the fast version have options for normalisation 
> other than the default quantiles? QN is good for merging replicates, 
> which should all have the same distribution. However, it introduces 
> artifacts when comparing chips from different conditions which are 
> observed to have different distributions.
> 
> 	Is it possible to have a quick version for just the 
> background calculation? And possibly another quick version for 
> the median polish expression summary? But I think the normalisation 
> choice should not be hardcoded.
> 
> 	Or is this heresy?
> 
> 	Thanks again,
> 		Harry
> 
>