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Animal-level prevalences and confidence limits, based on pooled samples, were estimated by using a pooled prevalence calculator (www.ausvet.com.au/pprev).au/pprev
Finally, we considered estimation of animal-level prevalence based on pooled samples.
Although several RNA-seq experiments, based on pooled samples of RNA, have identified DEGs [ 25], the validity of pooling for RNA-seq experiments to detect DEGs has not been systematically evaluated so far.
Note that the absolute values of our diversity estimates are not directly comparable to other studies in chicken, because we used NGS data based on pooled samples rather than Sanger sequencing data and we employed stringent filtering criteria.
Our N. ceranae spore counts were based on pooled samples of 20 bees using the standard methods and were highly variable between colonies, as is typical for this species (Meana et al., 2010; Mulholland et al., 2012), but no significant difference (Kruskal Wallis, d.f. = 3, H = 1.37, P = 0.7) was detected between the four islands.
Importantly, the tree based on pooled samples (Fig. 4) was the same as the tree based on individual samples (Fig. 3).
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These inferences have often been based on "pooled" data.
On this basis, the first 2000 samples of each chain were discarded as 'burn-in'; each chain was run for a further 10,000 iterations, and posterior estimates were based on pooling the 5 × 10, 000 samples for each model.
A detailed look on the setup of the microarray hybridizations (Additional File 1) reveals, that four profiles (n24h-1, 2, 3, 5) are based on pooling of samples from a mock inoculated and an untreated udder quarter, while the profile n24h-4 was obtained from a single untreated quarter.
Additionally, compared with the study by Rubin et al. [ 42], the different point is that the current study is based on individualized sequencing while that of Rubin et al. is based on sequencing of pooled samples.
Additionally, because the isoform annotation is based on pooling of reads from 27 samples, the distribution of this splice isoforms amongst the individual samples is not apparent in the current study.
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