Inter-site reproducibility
SEPARATION, BRAIN
The seminal SEQC study investigated the concordance of samples processed in multiple sites performing contrasts of two reference samples (Universal Human Reference RNA vs Brain Reference RNA). One important conclusion from SEQC was that while RNA-Seq fold-change estimates were generally concordant between laboratories, read-count data could not be reliably combined (In this study, we showed that the inter-site agreement between logSeveral groups have demonstrated that correlations are not sufficient to allow the combination of datasets generated at distinct sites (In addition to the aforementioned differences, global PCA and MDS analysis of LCPM across all 100 samples showed a strong separation of the two sites indicating that the data could not simply be merged, e.g., by using the sum of the read counts obtained for the two aliquots belonging to the same sample (