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Transcripts with a minimum fold expression change of two were selected as differentially expressed genes.
Applying a minimum fold expression difference of ≥1.25× relative to the NP and the requisite significance threshold (FDR 0.5%) reduced the number of cases of overdominance to 3,505 contigs (5.1% of all 68,746 contigs) and the number of cases of underdominance to 1,155 contigs (1.7% of all contigs).
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All genes were required to have a minimum of 2 fold expression and 100RFU for raw signal.
Genes identified to be differentially expressed had a minimum 2-fold expression ratio at any time point.
434 genes were identified using a Benjamini-Hochberg multiple hypothesis correction (p < 0.01) with a minimum 2-fold expression change.
Figure 2 shows the effect of introduced fold change (Fd), restriction on the minimum fold change (Fa) and expression level (Em) on the Sensitivity and Precision of the differential expression analysis.
Genes were defined as TB-associated if they met the following inclusion criteria: minimum mean TB expression ≥25, fold expression difference (TB versus LE) ≥5 with a p value ≤0.05.
We focused on the genes within the 73 genomic clones which exhibited a minimum threshold of ± 1.5 fold expression change (p < 0.005) between at least two treatments (Additional file 4).
The acceptance criterion for gene array expression changes was a minimum fold change of 2.0 and a t-test p-value of < 0.05.
The IsoDE test for differential expression requires two user specified parameters, namely the minimum fold change f and the minimum bootstrap support b.
A minimum fold change threshold was established by calculating the median standard deviation of rim/core expression for each biological replicate (n = 3).
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CEO of Professional Science Editing for Scientists @ prosciediting.com