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The second use case data set was based on "hypothetical" proteins in RefSeq.
First 500 samples with replacement were taken from the complete case data set.
Therefore, the base case analysis will be based on the MI, while the complete case data set will be used for the sensitivity analysis.
Although having only one case data set prevents us from measuring inflation due to genotyping errors among case individuals, given that the same quality control steps were used, we expect this to be of similar magnitude.
We then used logistic regression analysis to determine the effect size of rs10936599 according to the rank of the individuals in each case data set compared with all controls, stratifying by sex, age and study of origin.
In both the Australian and UK data sets, affected women completed a self-report questionnaire including questions about fertility history and pain symptoms; however, as questions were phrased differently, sub-phenotype analysis was limited to data from the largest case data set (QIMR, 2078 cases).
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Analysis of a complete-case data set alone cannot be expected to give reliable estimates of model coefficients without making assumptions about the missing data.
The use case data sets were derived from their original publications; the initial number of features and cases are the following: the protein corona data set [49] has 129 features and 84 cases, the metal oxide data set [50] has 32 features and 18 cases and the toxicity data set [51] contains 8 features, and 546 cases.
Sequence similarity data was creating using all-against-all BLAST comparisons within the training and test data sets, and between the training and test data sets and the use case data sets (redundant alignments were excluded).
σ Outbreak and case data sets are not mutually exclusive or encompassing.
Future analyses of this kind should aim to assemble case data sets with aggregation at the level of week or month as this will allow for a more detailed analysis of potentially lagged effects.
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