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Still, fluctuations among replicate experiments are large (the estimated among experiment variance is 3.012 which is larger than the estimated variance among selection lineages).
In our experiment, variance was fixed across reward levels, making the CV smaller for the decisions with high-value rewards.
18S amplification was only included in one experiment; thus, MSE-ANOVA for 18S only represents within experiment variance.
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These F-ratios were significantly smaller in the heterogenized design (F1,28 = 4.678, p = 0.039, Fig. 8), demonstrating that heterogenization did indeed increase within-experiment variation (variance among blocks of the same laboratory) relative to between-experiment variation (variance among blocks of different laboratories).
The repeatability standard deviation (SD) of the un-patterned sample, which quantifies the repeatability of the methods based on control variances, is the square root of the sum of the among-experiment variance and the within-experiment variance divided by the number of replicates per experiment [39].
The overall accuracy in the current experiment (0.95) was slightly lower than that in Experiment 1a (0.97), suggesting that the mask blocked certain information albeit it was not significant (t(29) = 1.16, p = 0.256) which may due to between-experiment variance.
The average within-experiment variance was larger in 23 out of 29 measures in DBA/2NCrl mice and in 18 out of 29 measures in C57BL/6NCrl mice, suggesting that heterogenization systematically shifted variance from between-experiment to within-experiment variation.
The inter-experiment variance was the parameter with the greatest source of measurement noise, accounting for an average 61.7% of the total variation in reported gene expression.
Estimates of the among- and within-experiment variances were assessed using ANOVA of the log transformed cell densities for each un-patterned control sample and micro-patterned sample, with a random effect for experiment.
To assess whether improved reproducibility in the heterogenized design was caused by heterogenization shifting variation from between-experiment variation to within-experiment variation, within-experiment variances were averaged across the six laboratories and compared between the two designs for each of the 29 behavioral measures.
Note that in this experiment, this variance will include variation due to flow cell as well since there is only one subject per response group per flow cell.
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