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Mathematical description—We first partition the space of permutations into blocks using some blocking function γA that maps each permutation to a real number; permutations with the same number are in the same block.
RP values, for each gene, were compared to the RPs of 1000 random permutations with the same number of replicates and genes as the real experiment.
The p-value of the permutation test was the proportion of permutations with the same or larger difference as those observed in the original data.
In our study we tested this value by permutations, with the same number of random genes sampled from the genome and the λ-value calculated (random λ).
The average amount of traces observed for circular permutations is bigger than the one observed for linear permutations with the same reversal distance.
The p-value for the observed number of significant tests was computed as the proportion of permutations with the same or a more extreme number of significant tests.
Similar(54)
For a more direct comparison, we also performed gene-level permutation-testing with the same software used for the multi-tissue analysis but with no inter-tissue dependence; this gave 126 cis-eQTLs in dura and 77 cis-eQTLs in blood (FDR < 0.01), with 32 shared by both tissues.
Pair-wise comparison of FST between populations of sampled Shortwings was also conducted with ARLEQUIN 3.11 [53] and significance values were determined with 1000 permutations in the same software.
This is a crowded space, dealing with lots of permutations of the same features.
Along the T nigroviridis and D rerio genomes, the distribution of windows has been compared with 1000 random permutations of the same windows.
Examining interactions predicted at 2 threshold levels: 2+DB and 3+DB, we created microRNA networks for both the canonical signalling pathways and for 2000 permutations of pathways created with the same number of primary node genes.
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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