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Y-axis depicts the log2 values of fold change (FC) in relative expression values (REV) of genes (mentioned on X-axis) between infested (RP-I) and un-infested (RP-UI) samples.
Mean values of fold difference for each cohort used here were compared to those obtained previously [4] (Figure S1).
Mean values of fold difference for each cohort were compared to mean values obtained for pools analyzed by microarray hybridization.
The mean values of fold increase among groups were compared using student t- test and the Mann Whitney U Test as the variance between groups was high.
The absolute values obtained on day 12 for EROD or BROD activity were divided by the baseline activity on day 4 to obtain values of fold change.
Briefly, the amplification of FcεRI-α gene in stimulated cells was calculated first as the copy number ratio of FcεRI-α to GAPDH, and then expressed as normalized values of fold increase over the value obtained with unstimulated (control) cells.
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The presence of a binder (gum Arabic) which provides initial strengthening of paper pad, was the reason of heightened values of folding endurance.
Genes were scored as over-expressed or under-expressed if their value was respectively above or below cut-off values of fold-change respect to mean value.
In summary, this strategy results in the following advantages: The normalized ranking approach enables comparability across data from different studies, platforms, and analysis methods by removing dependence on absolute values of fold-change, minimizing some of the effects of normalization methods used, and accounting for platform effects.
The threshold values of fold-change were usually set at ≤0.667 or ≥1.5.
This filtering criterion based on cut-off values of fold-change provided a pool of candidate genes differentially expressed.
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