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In the modified Mantel test, diagonal elements of both matrices were excluded from analysis as only elements of between-family prediction accuracy (off-diagonal elements) and not within-family prediction accuracy were of interest.
Some elements of the model matrices were excluded from contributing to the correlation as they were not relevant to the hypothesis being tested (N/A values in Figs 3 and 5).
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Peptides with masses correspondent to those of trypsin and matrix were excluded from the peak list.
*Subjects who showed an MTrP located outside the matrix were excluded from the analysis.
Regions of uncertain alignment in the 190-taxon-matrix were excluded prior to analysis (161 nt from the beginning,76 nt from the end and 7 nt fragment at position 814 of original alignment).
Where a matrix used estimated rather than raw counts, as indicated by the occurrence of a decimal point in the 'frequency' matrix, that matrix was excluded (as we have assumed that raw counts will be used).
To condense the overall size of the matrix, rows were excluded if all columns were empty.
TFs for which no PBM-derived matrix was available were excluded.
For a given data matrix, the rows were excluded if more than 40% of missing values were observed.
The output of this analysis is a 61 by 61 matrix termed the 'codon bias matrix' (the three stop codons were excluded from this matrix).
Finally, replicate reproducibility was estimated by using scatter plots and a Pearson correlation matrix, and any clear outliers were excluded from further analysis (Figures S1A, S1B and S1C).
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Justyna Jupowicz-Kozak
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