[BioC] justGCRMA normalisation options?

[James MacDonald]

Also note that justGCRMA will likely not be faster than gcrma, and the
devel versions of both are much faster due to the introduction of some C
code (thanks to Jeff Gentry). If you have the memory to run gcrma, and
are adept at hacking code, you could just modify gcrma.engine() to
return the background corrected AffyBatch and then feed this to
expresso. Because of the way justGCRMA works, it would take a bit more
work to change how the data are normalized, so if you have the RAM,
gcrma is probably the way to go for now.

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "Rafael A. Irizarry" <ririzarr at jhsph.edu> 03/19/04 11:20AM >>>
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
> 
>

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