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EEMF data sets acquired for these calibration sets were subjected to MCR-ALS analysis.
The data sets were subjected to exploratory analysis to identify the outliers and carried out different transformations such as log normal and square root to ensure normal distribution.
Three different charges i.e., GH, AM1BCC and MMFF94 were applied to the dataset and all three sets were subjected to the database alignment by using sybyl7.3 [16].
Data sets were subjected to multivariate statistical techniques: two-way analysis of variance (ANOVA) and Tukey's t test were used as a post hoc analysis to compare the means (Zar 2009).
The resulting candidate survival probe sets were subjected to a supervised analysis [16], which comprises computation of principal components with candidate probe sets, Cox proportional hazards regression analysis using the resulting principal components, and finally prognostic predictor calculation by fitting the predictive prognosis model derived from the Cox regression.
All data sets were subjected to both pairwise and ranked correlation calculations.
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Each of these simulated data sets was subjected to ML and MP analyses.
This set of 17778 probe sets was subjected to Significance Analysis of Microarrays (SAM) analysis [84] (http://www-stat.stanford.edu/~tibs/SAM/, which utilizes a Wilcoxon-test statistic and sample-label permutation to evaluate statistical significance between sample groups.
Each of the three tumor + N data sets was subjected to hierarchical clustering analysis using the 22 cell cycle-associated genes.
Each of these data sets was subjected to unweighted maximum parsimony (MP) and maximum likelihood (ML) analyses using PAUP *4.0b8 [ 41].
The normalized peak intensities in the blinded set were subjected to analysis.
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