Hi all,

 

Has anyone tried validating RMA and GC-RMA in Stratagene's ArrayAssist
Lite software against the Bioconductor implementations? ArrayAssist Lite
is appealing in that it's free and capable of performing these methods
on massive numbers of CEL files on a desktop computer with limited
memory-it just takes a really long time.

 

I typically use the Bioconductor implementations of RMA/GC-RMA, so I
wanted to make sure that if I generated data in ArrayAssist Lite it
would be comparable. Despite using what appear to be the same parameters
for these methods with both software packages, the results are not
coming out the same. For RMA, the Pearson correlation of the log(signal)
coming out of the two methods is R=0.997, with slight disagreement in
values at low signal values. For GC-RMA, I'm getting R=0.98, and in the
low signal range ArrayAssist Lite is showing much higher signal for some
probe sets. Here are the software versions and parameters:

 

Bioconductor:

justRMA() function from affy version 1.5.8, default parameters

justGCRMA() fuction from gcrma version 1.1.3, default parameters

 

ArrayAssist Lite 3.3, default parameters for both functions

 

I'd appreciate hearing about experiences anyone has had with this sort
of comparison, or any feedback on where I may be going wrong.

 

Thanks,

Bruz


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