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The sensitivity and specificity of the PET methods indeed greatly depends on the use of quantification methods [ 15, 25, 26].
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We used 4 types of quantification methods to estimate mRNA expression levels.
In addition to the dataset generated as described above, two additional data sets were used in the comparison of quantification methods shown in Fig. 3.
Spiess et al. found that log-logistic models often perform better at data-fitting than logistic models [11], so 4 and 5-parameter log-logistic functions were used in our comparison of quantification methods.
The choice of quantification method used depends on user requirements.
Considering the large number of CNVs reported (>6000 entries in the database of human variation) the number of validated CNVs using independent quantification methods such as RT-qPCR or FISH is still proportionally very small due to the time consuming or limited throughput of single locus analysis.
The fold induction of GS mRNA was calculated using the Relative Quantification Method of the Light Cycler 4.05 software (Roche Diagnostics GmbH).
The quantitative values of the genes of interest were normalized using Gapdh as the endogenous reference, and fold-increase over control values was calculated using the relative quantification method of 2−ΔΔCt.
Gene expression was quantified using the relative quantification method of Livak [71].
The expression of Flk1A, VEGFA2 mRNA was normalized to the amount of bactin1, using the relative quantification method described by the manufacturer.
We obtained some values greater than 100% for estimated % human DNA content, which may be explained by our use of a ratio of two different quantification methods, each with substantial variance.
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