The Z or T statistics may be reported by component (discrete/continuous) when combined='no'
or combined by Fisher's or Stouffer's method (combined='fisher'
or combined='stouffer'
.
Fisher's method uses the product of the p-values, while Stouffer's method uses the sum of the Z/T scores.
The "Z" score returned by Fisher is the normal quantile that would yield the observed Fisher P-value, whose sign is derived from the sign of the maximum component Z score.
The "Z" score returned by Stouffer when testType='normal'
is the sum of the Z scores, over sqrt(2).
When testType='t'
it is a weighted combination of the Z scores, with weights correponding to the degrees of freedom in each of the t statistics.
A t-approximation to this sum of t-variables is derived by matching moments. It seems to be fairly accurate in practice.
calcZ(gseaObj, testType = "t", combined = "none")
gseaAfterBoot
character
one of 'none', 'fisher' or 'stouffer'3D array with dimensions set (modules) comp ('cont'inuous or 'disc'rete) and metric ('Z' stat and two sided 'P' value that P(z>|Z|)) if combined='no'
, otherwise just a matrix.
gseaAfterBoot
## See the examples in gseaAfterBoot example(gseaAfterBoot)#> Warning: no help found for ‘gseaAfterBoot’