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The model terms with default parameter values are outlined in Table 1.
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Differentially expressed probe sets were analyzed for Enrichment of Gene Ontology Terms by GOEast with default settings (Zheng and Wang 2008), including a calculated (Benjamini and Yekutieli 2001) FDR threshold of 0.1.
Formal semantics of theoretical terms in scientific theories with default axioms are presently being developed.
Functional analyses of the genome-wide data were conducted using the CGD GO (gene ontology) term finder [ 57], with default parameters.
According to the NCBI-nr annotation results, the top BLASTX hits were used to identify putative homologous proteins and annotate each TAC with gene ontology (GO) terms using Blast2GO [ 48] with default parameters.
The projected GO annotation (Additional file 8: Table S7) [ 55] for the differentially expressed probes was then analyzed for enrichment of Gene Ontology (GO) terms using GOEast [ 56] with default settings (adjusted p-value < 0.1).
We used this annotation information to perform GO enrichment analysis of all 66 genes under positive selection in H37Rv annotated to at least one GO term (57 genes) when compared with all 3108 valid genes from FILTER experiment that are annotated to at least one GO term (2600 genes) using BINGO with default parameters and a cutoff q-value <0.05 [ 55].
Nowhere near as serious as moustaches or Hitler, I've recently had to come to terms with the popularization of my default wintertime sartorial style by one of the Republican candidates for President of the United States in the person of former Pennsylvania Sen. Rick Santorum -- namely the sweater vest.
By default, enriched terms with p-values less than 0.05 are presented in an interactive bar chart generated with Google Chart Tools [ 37].
The Bioconductor globaltest package (version 5.0.1; [ 37]) was used for testing the association of GO terms with microarray samples, using the default regression model.
Fed up with what she terms "the default world", Sarah Wu left America nearly a decade ago for the jungles of Costa Rica.
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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