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PLS obtains a linear regression by projecting the input and output variables to a new space and addressing collinearity by reducing the number of variables, removing those which are least important for prediction.
In order to increase the power of statistical testing for detecting differential expressed genes, we performed pre-filtering of features removing those, which never show expression over 6 in log2 scale.
To further bind the two lists, we pruned the list of significant gene sets by removing those which are not overrepresented in the list of significant genes, as assessed by a hypergeometric test with a cut-off of q<0.05.
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Many windows were broken already, and the prudent thing would have been to remove those which remained, but it was winter and the nights were cold, and without gas and electricity, both of which were in increasingly short supply, windows served to take some of the edge off the chill, and so people left them in place.
We compare our proposal against an architecture exploration technique, connectivity reduction, which finds in compiled application all interconnection network components that are used and removes those which are not, leading to an energy-efficient application-specific instruction-set processor.
To assess whether any characteristics which displayed statistical significance in univariate analysis were independently associated with improved outcomes, we combined any co-variates with a p value of ≤0.2 in a multivariable model and used a stepwise backwards elimination approach to remove those which did not contribute significantly to the model.
We identified falsely primed TC 3′ ends during the DeTCT analysis pipeline by examining the 10 bases 3′ of the TC 3′ end and removed those which potentially derived from non-polyA tail priming using the criteria described in the methods (see Additional file 4).
After removing those for which there was no ChIP or PPI data, we were left with 551 genes.
Then, we filtered subsequential patterns of genes in each dataset by removing those genes which are not in the integrative GIN.
We have prepared a new set from the Structure benchmark set by removing those proteins, which have 40%% or higher sequence identity with any sequence of the training sets used by the 10 prediction methods.
In comparison, determination of the tree took about 50 minutes with a ~880 MB HapMap format file because of the need to perform additional steps that involve testing each SNP position and removing those positions which do not have sufficient numbers of qualified SNPs for all 31 samples, described in the procedures above.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com