For the factorial designs, interest was in differential expression for the first factor, the other being a blocking factor.
For the DESeq/DESeq2 analyses, a two-factor linear model was fitted with the factors Sex and Year where Year was included as a blocking factor and the effect of Sex was tested after removal of the Year effect.
In each study, pre-treatment live flea counts were used as a blocking factor to randomize cats to treatment, and treated in the fed state, with flavored tablets containing either no active ingredient (control) or spinosad (50 100 mg/kg in the SOFK study; 50 75 mg/kg body weight in the SHE study).
Side of the fish cage was used as a blocking factor in the experimental design and had a significant effect on final oyster size; at the end of the study, oysters at the farm were either significantly larger or not significantly different than oysters at the reference site, depending on the side of deployment.
The experiment ran for three years, thus year was entered as a blocking factor.
Our previous studies indicated that time of testing influences behaviour in the 5-CSRTT (Yan et al., 2011; Weir et al., 2014) and so this was used as a blocking factor, to account for any additional variance in the data.
As before (Yan et al., 2011; Weir et al., 2014), certain behaviours (specifically, %omissions and %premature responses) depended on time of day, which was used as a blocking factor in the analysis of these behaviours.
Convergence rates were excellent for all models, with the worst case being non-convergence for four genes when a blocking factor was included in the model.
The full-field events image of the source in the second row of the results table is shown below, at a blocking factor of 2. The image displayed in Source Preview may be saved to a JPG file by selecting File->Save within the Source Preview window.
