For statistical reasons, genes that were not present in the entire microarray analyses were excluded from the related comparisons [ 17].
Sensitivity analyses excluding age from clinical model.
ML analyses excluded indels.
Phylogenetic analyses excluded gap regions.
From the original 180 samples, 148 provided sufficient quantity of high-quality RNA for microarray analyses; 13 additional samples were excluded because of technical problems.
It is therefore not only necessary to retain as many perfect match probes as possible, but also to exclude biased probes from microarray analyses.
This approach excluded signals from downstream alternative promoters, which complicate measurements in microarray analyses; confirm that a large proportion of these promoters are co-expressed from the neighbouring TSSs.
A possible explanation is that the Fe2+-Fur activated genes showed modest differential expression (approximately 2 fold) (Table 2), thus small experimental fluctuations could exclude some genes based on our cutoff criteria for differential expression in the microarray analyses.
We cannot exclude, however, the possibility that some of the changes in gene expression were due to the male fish employed in the microarray analyses being at different stages of the reproductive cycle at the time of sampling.
Work flow for microarray analyses.
