[BioC] Agilent Feature Extraction Software vs GenePix Pro

[Juan Carlos Oliveros]

Dear all,

In our group we are moving from GenePix Pro (scanner and sofware from 
Molecular Devices) to Microarray Feature Extraction Software (scanner 
and software from Agilent) to analyze two color arrays from Agilent. We 
use limma and Rank Products for detecting differential expression.

In our experience, for the same experiment (the same slides scanned and 
quantified with both systems):

logRatios tend to be higher (absolute values) in Agilent than in GenePix

log Ratio Standard Error measures tend to be higher in Agilent than in 
GenePix.

We obtain less significant results with Agilent equipment than with 
GenePix (at the same FDR threhold).

Our conclusion is that Agilent system is more sensible (actually its 
dynamic range is larger than GenePix) so small intensity differences are 
best detected than in GenePix scanner. As a result, the variability 
increases and the number of statistically significant genes decreases.

I would like to know if any one have compared these two popular systems 
and if they had similar results.

Thanks in advance.

Best,

Juan Carlos Oliveros, Ph.D.