[BioC] Agilent Feature Extraction Software vs GenePix Pro
Juan Carlos Oliveros
oliveros at cnb.csic.es
Tue Dec 14 13:10:12 CET 2010
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
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.
Juan Carlos Oliveros, Ph.D.
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