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 | AD∗w; \(AD=\overline {x_{1}} - \overline {x_{2}} \) | 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 | \(\frac {B_{1}+B_{2}}{2}\); \( B_{1}=\frac {1}{n_{1}}\sum \limits _{j=1}^{n_{1}}\frac {\left (R_{1}^{j}-\frac {n_{2}+n_{1}}{n_{1}}j\right)^{2}}{\frac {j}{(n_{1}+1)} \left (1-\frac {j}{(n_{1}+1)}\right) \left (\frac {n_{2}(n_{2}+n_{1})}{n_{1}}\right) }\) | ||
\(B_{2}=\frac {1}{n_{2}}\sum \limits _{i=1}^{n_{2}}\frac {\left (R_{2}^{i}-\frac {n_{2}+n_{1}}{n_{2}}i\right)^{2}}{\frac {i}{\left (n_{2}+1\right)} \left (1-\frac {i}{(n_{2}+1)}\right) \left (\frac {n_{1}(n_{2}+n_{1})}{n_{2}}\right) }\) | |||
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] |