[BioC] RMA question + GCRMA question

Rafael A. Irizarry ririzarr at jhsph.edu
Wed Aug 27 18:20:39 MEST 2003

we are constantly improving gcrma and until we have a final product, 
there will be no fast version.

prelimary results with spike in experiments suggest that gcrma is a bit 
more accurate than RMA. i feel quite optimistic about the model its based 
on, but the software implementation has not been tested thoroughly on 
other data sets. criticism/comments/suggestsion are greatly appreciated.

for this particular package you can interpret the version number 
smaller than 1.0 as an indication that it is still under development.

 On Wed, 27 Aug 2003 Phguardiol at aol.com wrote:

> thanks Rafael,
> another question, I guess GCRMA is going to be memory consuming in a 
more aggressive way than RMA ? is there a GCRMAexpress planned ?  
> I m currently testing it and it is for sure less fast than RMA... with 8 
chips (HU133A) it takes more time than with 40 chips under RMA ! By the 
way I have compared 2 differential analysis using either RMA or GCRMA all 
the other steps being done the same way with the same chips and some genes 
had some dramatic changes with GCRMA... SInce it will not be possible to 
check all these by PCR, is there any way to say which method is the most 
reliable one and reflects "reality" ? I bet you are going to say GCRMA...! 
Biological knowledge about these genes is the only way for me to go ahead 
but...it is limited !         

> Thanks
> Philippe

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