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Relative expression levels of target genes were calculated with normalization to β-actin values using the 2−ΔΔCt comparative cycle threshold method.
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Spectrophores were calculated with varying normalization parameters and stereospecificity settings, however with a constant default resolution of 3 Å and a constant angular step size of 20°.
Pearson correlation of two neighbours was calculated with log2-normalization (after addition of 0.05) of raw expression level (FPKM).
All spectrophores were calculated with stereochemistry and normalization flags both set to 'none'none
Besides the check for necessity of the bias update, Fig. 6 also provides a comparison of the "optimal" bias with the actual bias, both calculated with the same normalization.
Expression levels of selected miRNAs in saliva samples of these patients were calculated with U6 as normalization factor.
Expression levels of circulating miRNAs were calculated with miR-16 as normalization factor.
The qPCR expression data normalization was performed using normalization factors calculated with Genorm software (http://medgen.ugent.be/~jvdesomp/genorm/) from the GAPDH and the ACTB expression values.
Relative amounts of transcripts were calculated with the ΔΔCt method after normalization with endogenous control.
Variance stabilization was performed using the log2 scaling, and gene expression normalization was calculated with the method implemented in the lumi package of R-Bioconductor.
MicroRNA concentrations were determined by calculating ddCT with normalization to U6 snRNA.
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