Discordance of detection of DE genes between sites was mainly driven by differences in mean fold change
To assess and compare the strength of the biological signal, i.e. the change in magnitude of gene expression longitudinally over time (Days 1, 2, 7, and 14), we contrasted mean LFC and mean LCPM using MA plots (
These data were instructive for establishing the relative contribution of cutoffs to the discordance of DEGs between sites. We demonstrated here that by removing the FC cutoff criterion of 1.5 fold (in either direction), an increase in the inter-site agreement of DEGs by 20 percentage points was obtained. We hypothesize that the observed differences in fold changes between sites are attributable to differences in RNA representation in the aliquoted PBMCs.