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Representative scatter plots of microarray platforms and the Taqman system are displayed in Figure 2A (scatter plots for all possible combinations between three replicates were shown in Figure S4).
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Before comparison analysis of proteins expression levels, Pearson correlation between three replicates was performed to determine the analytical reproducibility (Additional file 4: Figure S2).
The variability in the CDS detection between two replicates was around 8%, except for ENC (11%).
If the coefficient of variance between two replicates was more than 20% the data was considered as a missing value.
Overall the arrays appeared to be very reproducible; images of the arrays, including spot intensity and quality, were well replicated and probe performance between two replicates was the same.
The number of time points that can be submitted to mirnaTA is a minimum of 2 to a maximum of 20. mirnaTA is able to handle to three replicates as follows: if the correlation coefficient (r) value between two replicates is more than or equal to 0.70, the count values from replicates are averaged and used in the study.
Samples were excluded from the analysis if the coefficient of variation between the three replicates was <0.1.
The Spearman's correlation coefficients (Rs), and the coefficient of variation (CV) between the three replicates was calculated using the 309 common microRNAs.
Concordance between the three replicates was strongly correlated with microarray signal strength, ranging from virtually 100% for the most strongly expressed genes to almost 0% for the most weakly expressed genes.
The correlation between the three replicates was very good, with an interclass correlation coefficient of 0.97.
Proteins with a high coefficient variation (CV) between the two replicates were discarded.
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