Fig. 2.

degCheckFactor analysis of the proportion of the normalized counts for each gene relative to its mean count across the different sections (intra-section) or all same sections (inter-section) from the Simulated-TOMOSeq data and the resulting Principle Component Analysis for the 5000 genes showing the most variance. Replicate number is represented as r, a given egg section as s and gene as z. Intra-section analysis shows how well the normalization technique maintains separation between the different sections, while the inter-section analysis shows how well the median-of-ratios method can normalize between replicates.