Skip to main content

Table 2 Description of ranking metrics sorted from the most parametric, through non-parametric to data mining methods

From: Ranking metrics in gene set enrichment analysis: do they matter?

Metrics Description Comments Ref.
T-test \(\frac {\overline {x_{1}} - \overline {x_{2}} }{\sqrt {\frac {{s_{1}^{2}}}{n_{1}}+ \frac {{s_{2}^{2}}}{n_{2}}}} \)   [9]
MWT \(\frac {\overline {x_{1}} - \overline {x_{2}} }{se_{m}}\); \( {se_{m}^{2}}=\frac {d_{0}{s_{0}^{2}+d_{w}{s_{w}^{2}}}}{d_{0}+d_{w}}\) and absolute value [35]
MSD \(\left \{\begin {array}{ll} {CI}_{left} & log(FC)>0 \\ -{CI}_{right} & log(FC)<0 \end {array}\right.\)   [41]
S2N \(\frac {\overline {x_{1}} - \overline {x_{2}} }{s_{1}+s_{2}}\) and absolute value [9]
WAD ADw; \(AD=\overline {x_{1}} - \overline {x_{2}} \) and absolute value [39]
  \(w=\frac {\overline {x}-min}{max-min} \); \(\overline {x}=\frac {\overline {x_{1}} + \overline {x_{2}} }{2} \)   
Difference \(\overline {x_{1}} - \overline {x_{2}}\)   [9]
Ratio \(\frac {\overline {x_{1}}}{ \overline {x_{2}}}\) and log2 [9]
FCROS \({Mean}_{(truncated,10\%)}\left |\begin {array}{ccc}{FC}_{1,1}&...&{FC}_{1,k}\\.&&.\\.&...&.\\.&&.\\FC_{N,1}&...&{FC}_{N,k}\end {array}\right | \)   [40]
  k - pairwise comparison; FC - fold change, N - no. of genes   
SoR \(\sum \limits _{i=1}^{N_{1}}R_{i}\) ; N 1 - size of group 1; R - ranks of elements from group 1   [31]
BWS \(\frac {B_{1}+B_{2}}{2}\); \( B_{1}=\frac {1}{n_{1}}\sum \limits _{j=1}^{n_{1}}\frac {\left (R_{1}^{j}-\frac {n_{2}+n_{1}}{n_{1}}j\right)^{2}}{\frac {j}{(n_{1}+1)} \left (1-\frac {j}{(n_{1}+1)}\right) \left (\frac {n_{2}(n_{2}+n_{1})}{n_{1}}\right) }\)   [31, 36]
  \(B_{2}=\frac {1}{n_{2}}\sum \limits _{i=1}^{n_{2}}\frac {\left (R_{2}^{i}-\frac {n_{2}+n_{1}}{n_{2}}i\right)^{2}}{\frac {i}{\left (n_{2}+1\right)} \left (1-\frac {i}{(n_{2}+1)}\right) \left (\frac {n_{1}(n_{2}+n_{1})}{n_{2}}\right) }\)   
ReliefF \(W-\frac {\sum _{k=1}^{K}D(x,h_{k})}{tK}+\sum \limits _{c\neq class(x)}^{} \frac {P(c)}{1-P(class(x))}\frac {\sum _{k=1}^{K}D(x,m_{k})}{tK}\) and tied rank [38]