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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.
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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.
Strikingly, these patterns capture both dose effects in the mouse experiment and strain differences in the macaque experiment.
Second, since the observed differences in the previous experiment could be a direct consequence of leptin deficiency, we repeated the experiment (Figure 5, A) using db/db mice [30], [34] and their littermate controls.
In some cases, scientists apply artificial treatments to create the difference in the experiments, and facilitate the comparison [ 8, 9].
The conflicting results may be explained by the differences in how the experiments were performed.
Thus, we have more power to detect expression differences in the male experiment.
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