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with six pulses of 30 s each at the maximum setting (Library 1 and 2) or using a Covaris S2 (Covaris) for 8 minutes with the following settings: duty cycle: max, intensity: max, cycles/burst: max (Library 3, TBP, H3K4me3).
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For the multiple tissue data set, the performance of BEEM depends on the type of input gene set libraries; SSA works better for the TF binding motif gene set library while BEEM works better for the curated gene set library.
A gene set library is assumed to have positive gene sets, and negative gene sets.
The TF binding motif gene set library was prepared as described in [6].
The curated gene set library including 1892 gene sets was downloaded from a gene set database, MSigDB [15].
On the other hand, the curated gene set library contains miscellaneous 1892 gene sets extracted from original literature [15].
As input gene sets, we prepared two types of gene set library: TF binding motif gene sets and curated gene sets.
A set of simulated data consists of an expression matrix and a gene set library containing positive and negative gene sets.
Taken together, our data suggest that the performance of SSA for the TF binding motif gene set library is artifactually enhanced by its gene set-size dependent property.
For the four analyses of different combinations of input gene set library and expression data set, we drew the heatmaps of p-values of all gene sets obtained by the three methods (Figure 6).
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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