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We estimated the accuracy to be 99.6% on average, and after excluding one sample because of multiple inconsistencies with the inheritance pattern expected on the basis of the declared pedigree, the genotyping accuracy increased to 99.8% on average, showing the high genotyping quality of the Carp array.
> -wrap-foot> The number of samples recovered (excluding one sample per replicate pair) after de novo assembly and quality filtering was 2 for B. trifolia, 9 for B. moranensis, 4 for the Cerro Zamorano population, and 6 10 for each B. alpina population (supplementary table S1, Supplementary Material online).
Having fixed the value of the free parameter k, the considered DR algorithm provides a two-DR for each leave-one-out step, excluding one sample from the training dataset in each round of LOOCV (nine samples in the dataset provide nine DRs during the leave-one-out procedure), and then estimating a proposed cluster validity measure (CVM) (Stein et al., 2003) in the 2D reduced space.
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We excluded one sample of the diseased group from further analysis of microarray data since miRNA expression levels were extremely different to others even after normalization.
The results of the quantitative real-time PCR showed that contamination of the positive samples equalled approximately three oocysts per sample, excluding one extreme (sample no. 187, contaminated with 19 oocysts) (Table 1).
However, even after applying the correction, the corrected Hg-values are still very high for the non-exposed individual AG93, RC t = 4.7 (test for RC t = 1: t = 4.91, df = 4, p = 0.002), which is calculated excluding one anomalously high sample, again this sample originates from a bone surrounding the central cavity of the body, a rib.
Sensitivity analysis was performed to detect the effect of any one of the included trials on the overall estimate by excluding one of them according to sample size.
Finally, to assess a possible relationship between GC content and capture efficiency, we subset the single baits that are apart from any other baits by at least 120bp and then calculated mean read depth across all samples (excluding one clone with a low percentage of mapped reads – see Results section) as well as the percentage of guanine and cystosine residues in each target region.
Group samples with gene expression correlation coefficients ≤0.95 were excluded (one KO sample).
As described in the Methods section, 15 patients per group were included in the analysis (except for the HITChip analysis, in which we excluded one outlier sample in the treated group).
Based on this quality check, we had to exclude one of the triplicate samples from further analysis (EPSmin17 experiment, Sample B) as it did not cluster with the other two EPSmin17 samples (Additional file 14).
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