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To focus our research on the potential value of these newer PPI network-based methods we excluded methods requiring additional information beyond a priori PPI knowledge.
Using PCR-based methods, we excluded the following as causative agent: mink enteritis virus, canine distemper virus, Aleutian mink disease virus, mink orthoreovirus, and mink coronavirus.
For all methods, we excluded rare SNPs (true allele frequency less than 5% in the CEU population of the HapMap, ) and the 5% of SNPs showing the highest technical variability as indicated by the size of the standard deviation amongst measures from the replicate arrays.
When the genotype results in an individual were inconsistent using both methods, we excluded these individuals from further analyses, even thought the HEA BeadChip is known to be more accurate than the AS-PCR [52], [53].
As noted in the methods, we excluded cheap instant coffee from vending machines from this analysis.
Lastly, for the purposes of this methodological study on imputation methods, we excluded the 351 participants of our surgical outcomes study who had truly incomplete SDS questionnaires.
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To more fairly compare the prediction methods, we exclude the 226 proteins from Set600 that share >90% sequence identity with the CMAPpro training set.
Since this Table measures the prediction performance of our machine learning method, we excluded all data for validation compounds from the respective training sets.
Therefore, in the implementation of the weighting method, we excluded the p-values which have been already statistically significant.
To investigate the influence of poor quality genotyping on the performance of the super-locus method we excluded any SNPs considered to be of low quality, based on clustering, from the gene region under study and re-analysed.
With the hold-out-sample method, we excluded a subset of the calls, which then had to be classified by the rest of the sample; 62.3% (63.4% including males) were correctly classified confirming that a random sample was possible to assign individually to the trained sample.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com