Open report_index.html in the output folder. The report
can be read in a browser without R. For Riaz ON, select
responders_vs_pd_on and open a LISA plot such as
GOBP-C2.
Each row represents a biological category. Its mean NES summarises the individually significant gene sets assigned to it. For Riaz ON, a positive NES points towards CR/PR responders and a negative NES towards PD.
The category mean is descriptive. It is not a measure of pathway activity, and the number of contributing gene sets is not the number of patients.
Select the category to open its evidence page. Look at the individual gene sets and their genes before interpreting the category label. Related sets often overlap, so several sets need not represent independent findings.
The category-significance view shows stars for adjusted category P values. Stars indicate evidence that at least one member set is enriched, not the size or direction of an effect.
The category card also reports d/N: at the default confidence level, at least d of N evaluable member sets are supported as enriched with 95% simultaneous confidence. This is a lower bound, not the exact count. An unmarked category can be nonsignificant or not evaluable; the card distinguishes the two.
The statistical analysis guide explains how these quantities are calculated and which hypotheses are assessed together.