The influence of the protocol on gene expression. All genes that are affected by the modifications to the protocol, either as a single effect or as an interaction effect, are analyzed. First, the mean expression levels of these genes across all 55 conditions are computed. The genes are divived in seven groups based on their mean expression levels such that each group holds the same amount (i.e. 14,3%) of the genes. Each group is characterized by a lower and a higher bound on the expression value; these two numbers represent the range of the mean expression levels of the genes within the group. Also, we dichotomize the genes into the ones with positive regression weights (i.e. upregulation under Protocol B with respect to Protocol A) and the ones with negative regression weights. a: The blue bars indicate the percentage of genes with positive regression weights (higher under Protocol B) across these groups (or expression ranges). Similarly, the red bars indicate these percentages for the genes with negative coefficients (higher under Protocol A). b, c: For the same ranges, each bar represents the percentage of genes in the range annotated to a particular functional category over all of the genes that are annotated with this category and affected by the protocol.