One might also be concerned that DNA microarray measurements of meagerly expressed genes would have a different degree of "compression" than measurements of genes expressed abundantly, so that, on average, the log ratios of one or the other would be inflated.
Why were previous measurements so useless?
Highly variable microarray experimental conditions and the use of different microarray platforms cause poor reproducibility of microarray measurements within and between laboratories [7] [11].
The sensitivity threshold of microarray measurements defines the concentration range in which accurate measurements can be achieved.
Microarray measurements were confirmed with real-time quantitative polymerase chain reaction (qPCR).
Several approaches for integrating microarray measurements with network knowledge were described in the literature.
When microarray measurements of differential expression are compared to qPCR, it is well known that microarrays provide a smaller dynamic range [3].
Technical validation of microarray measurements of gene expression was done with qRT-PCR and has been reported [34].
We used the affy package in Bioconductor [35] to read in and normalize the microarray measurements for each RNA type.
In total, 180 microarray measurements were performed.
