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A cluster analysis of the different microarray experiments also showed the consistent and specific upregulation of diverse MHC II genes upon CNOT2 knock-down compared to the various control samples, as well as the reproducibility between the replicate samples (Fig. 4B).
The software also calculates the coefficient of variation between the replicate samples.
In this quality control there was 100% concordance between the replicate samples and genotype calls between the independent evaluator.
On the ENCODE set, the number of DP calls between the replicate samples is also lower than that between the non-replicates.
MS Excel was used to calculate the correlation coefficients between the replicate samples based on the normalized, scaled and log2 transformed data.
The means for sample 1 and sample 2, replicates for the candidate WHO IS, were 5.58 log10 and 5.60 log10 copies/mL HEV RNA, respectively, with good agreement between the replicate samples.
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A ΔCq value was calculated reflecting the difference between the average Cq of the replicate samples obtained for the control gene (18S) and the average Cq of the replicate samples obtained for the test gene to be validated.
The absolute value of the difference between the replicated sample size calculation and the authors' target sample size was greater than 10% for 47 articles (30%) and greater than 50% for 10 (6%).
Correlation between the two replicate samples was high (r = 97.97%) so that they were merged.
For each microarray platform, we applied GSEA to generate hypotheses regarding which biological processes or pathways might be responsible for the differences between the two replicate sample pools.
The comparison between replicate samples one (as used in the main text) is indicated on the left, the comparison between combined replicate samples is indicated at the center left, the comparison between ES cell replicates is indicated at the center right and the comparison between E10.5 forebrain replicates is indicated on the right.
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