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A microarray experiment only measures the "observed" quantities, as shown in Figure 8, whereas the other quantities are not observed ("hidden").
While ISG15 was identified as being differently expressed (FDR = 1%) between fish injected with pIC at 10 vs. 16°C at 24HPI in the microarray experiment, only a non-significant change in the same direction was observed in the QPCR at 24HPI.
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The 200 ng/ml treatment was used for the microarray experiments only.
To reduce the cost of microarray experiments, only 46 animals randomly selected for AF values from the 71 BC2 male offspring were studied.
Across all 23 microarray experiments, only 99 probes (0.6%) did not show a signal higher than the background, while 14,274 (95.7%) were successful (flag value equal to 1) in at least 16 out of 23 experiments.
In addition, DNA microarray experiments only interrogate transcriptionally-regulated genes, so it is inevitable that a significant portion of false positive and false negative interactions in an inferred network will be generated.
One of the genes (m2) showed strong (1.7-fold) Europe over-expression in the microarray experiment, but only slight (1.2-fold) Europe over-expression by qRT-PCR.
Furthermore such a microarray experiment replaces only two steps in our mapping procedure, namely the pooled PCR and its associated gel run, which represent only a minor part of the total mapping effort, as compared to fish breeding, sorting of F2 embryos and confirmation of the bulked segregant results by genotyping of F2 individuals.
Of note, microarray experiment will only identify genes that are regulated at the mRNA stability levels by miR-34a and not the genes that are regulated through changes in translation.
Previous microarray experiments identified only 34 genes whose expression was up-regulated (>2-fold) in ρ° petite cells (which do not have mtDNA) compared to ρ+ cells [27].
Newton et al. [ 6] proposed another empirical Bayes model for cDNA microarray experiments with only one replicate.
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