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Instead of comparing the scree plots of newly generated datasets with that of the original one, we used the distribution of percentages explained by the first two components in random datasets to assess the significance of components extracted in the original dataset.
We compared its fusion prediction performance on these two datasets with that of TopHat-Fusion v2.0.3 (Kim and Salzberg 2011).
We compared the performance of the BBC algorithm for several different types of simulated datasets with that of the plaid model [ 5], the ISA [ 4], the method of Cheng and Church [ 1], the SAMBA method [ 6] and the OPSMs [ 7].
We computed the Pvalue by randomly permuting 999 times the values of the outcome and comparing the measures of association of the covariates in the permuted datasets with that from the original dataset [ 35].
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The high (R2 = 0.943) coefficient of determination fits well with the experimental dataset with that of the ANN model of the system (Yang et al. 2011; Khataee et al. 2011).
We compared the distribution of GO annotations in our dataset with that in the whole yeast genome and tested for significant deviations (Methods).
To assess whether drug treatment acts as the consistent amino acid selection in these two datasets, we compared the (A,A) covariation in the Treated dataset with that in the Untreated one.
We then compared the R values computed from our dataset with that for 10000 random groupings of the TF genes in families, matched for family size of the actual dataset.
It is more appropriate to compare the quality of the M. tuberculosis H37Rv B2H PPI dataset with that of other B2H PPI datasets; but such large-scale reference B2H PPI datasets are currently not available in public databases.
Lastly, the χ2 test between the Hg frequencies of the complete ancient dataset with that of the complete Scandinavian (not only considering native breeds) demonstrated a significant deviation between the modern and ancient frequencies (p < 0.0388, χ2 = 4.27, df = 1).
Additionally, Lopez Herraez et al. [ 51] had genotyped five individuals from each HGDP population, including five Biaka, using the Affymetrix GeneChip Human Mapping 500 K array set, concatenating this dataset with that of the Illumina chip [ 51].
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