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In some cases, scientists apply artificial treatments to create the difference in the experiments, and facilitate the comparison [ 8, 9].
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It is difficult to see the differences in the experiments were cells are pressed by slides.
Our results were in line to those of Kitaba et al. [ 13], despite several differences in the experiments performed.
Given differences in the experiments, we used Distance Weighted Discrimination (DWD) [ 17] to minimize systematic microarray data biases attributable to RNA source, different analysis laboratories, different microarrays, or other systematic differences which include sex and strain in this case.
The authors need to make explicit all the various differences in the experiments (sites, labs, equipment), and then they can use this as a 'strength' as they argue in their rebuttal.
This illustrates that there is greater similarity between the expression profiles of the two cell lines than there is between technical differences in the experiment (i.e. the two different microarray formats).
Five out of the 6 largest differences in the experiment was observed (2.6; 2.7; 3.3; 3.3; 4.2) for pig 25 and already on PID 0 the difference was 2.1 indicating that there was a systematically large difference in the measurements.
A difference in the two experiments is that Bachar et.al. evaluated islet cells in 3.3 mM vs. 22 mM glucose, and our experiments assessed cells in 5.5 mM vs. 25 mM glucose.
The level of disease resistance exhibited little year-to-year difference in the field experiments.
However, we do not find a functional significance for this difference in the field experiments, so do not consider it a critical issue.
The large differences observed in the experiments reported in Table 5.24 reflect the differences in the methodology applied and in the way the viability of metacercariae are determined (visually or by artificial infection in laboratory animals).
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