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To avoid BG fluctuations effects, the background level was subtracted from the expression measure, and any expression level below this cutoff was set to 0. This subtraction considerably reduces artificial correlation between weakly expressed ORFs.
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Scores equal to or below this cutoff were categorized as high risk while scores above the cutoff were categorized as low risk.
Values below this cutoff were assigned a value of 1 log10 copies/mL.
All values below this cutoff were given a different color for both the experimental conditions and the genes.
For BLASTX, an e-value cut-off of 10-15 was used and the sequences with e-value below this cutoff were then subjected to BLASTN analysis with e-value cutoff of 10-20.
When any of the algorithms is used, it is desirable to set a p-value cutoff so that, in the positive data, the number of intergenic regions that have values below this cutoff is large and, in the negative data, the number of the intergenic regions that have values below the cutoff is small.
This cutoff is far below that required to make a diagnosis of food allergy (6 kIU/L-eggs, 32 kIU/L-milk, and > 100 kIU/L-wheat) [ 36, 37].
This cutoff is approximate and based on a statistical probability that approximately 97.8% of random measurements will fall below this cutoff, and is used to provide a quantitative separation between verified true respiratory motion and noise.
Any gene with an average expression value below the cutoff was considered as background and not used for calculation of the total number of rhythmic genes.
For every BLAST search the GI number of the top hit (if it was below the cutoff) was saved along with the GI number of the query sequence forming a GI pair.
To avoid having extremely skewed groups (e.g., 3 patients in one group versus 29 in the other), the number of patients either above or below the cutoff was at minimum 1/3 of the patient sample.
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