What are the differences between significance, effect and standard deviation upon producing mitch reports?

Question

[Amr]

What are the differences between significance, effect and standard deviation upon producing mitch reports? for example, regarding differences in outputs and usage of each of them

Thanks

Answer 1

[Amr]

Effect size helps readers understand the magnitude of differences found, whereas statistical significance examines whether the findings are likely to be due to chance.

End users can prioritise results in three ways; (i) based on statistical significance (low p-value), (ii) effect size (large S) or (iii) standard deviation (SD) of s values across contrasts. SD prioritisation may be of use when searching for gene sets with discordant regulation.

When prioritising by statistical significance, top gene sets are likely to be larger (contain more genes) but more dispersed; while prioritisation by effect size emphasizes smaller gene sets with larger magnitude changes.

Sorting gene sets by SD of s values reveals several gene sets that exhibit stronger downregulation in DESeq2