More rice orthologs (13,070) were identified in comparison to Arabidopsis (10,776) possibly owing to a larger genome in rice, and there was an increased pool of reference species.
But as artists, as observers and chroniclers of life by way of prose, we go beyond that pool of reference.
First, we determined the transcript expression profiles for brain RNA from the dominant, sub-dominant and submissive specimens from each of 6 stable replicate hierarchies, using a reference-based experimental design based on single pool of reference RNA from all samples.
In order to estimate the adjustment factor γ k, a pool of reference samples is needed.
However, CNVhac needs a pool of reference samples to estimate γ k for calibrating amplification efficiency.
Removing the least stable gene, RNPS1, from the pool of reference genes only marginally affected the results (p = 0.024, Table 4).
The μ ^ = [ μ ^ l ] l = 1, …, L and σ ^ = [ σ ^ l ] l = 1, …, L are estimated from a pool of reference samples as the coverage and variability patterns.
The selection of reference genes for this experiment was performed using a pool of reference genes (Supplementary file 3) and analysing their expression stability via the geNorm software (Vandesompele et al., 2002).
Enriching the pool of reference sequences by including previously identified variant allele patterns, followed by remapping, improved mapping efficiency, raising coverage by 50% from regions with the greatest deviation, resulting in a coverage pattern indistinguishable from controls.
