MrTomRod
commented
3 months ago Dear @Ultramancc
Sorry for responding so slowly, I was on holiday.
Good question, the cause is a recent change that was made to Scoary2 in response to this issue/pull request:
The original behaviour (Scoary1 and Scoary2 up until 0.0.4):
- The sensitivity of using the presence of this gene as a diagnostic test to determine trait-positivity:
g+t+/(g+t++g-t+) - The specificity of using the absence of this gene as a diagnostic test to determine trait-negativity:
g-t-/(g+t-+g-t-)
The current behaviour (Socary2 starting with 0.0.5):
If gene and trait are positively correlated (original behaviour):
- The sensitivity of using the presence of this gene as a diagnostic test to determine trait-positivity:
g+t+/(g+t++g-t+) - The specificity of using the absence of this gene as a diagnostic test to determine trait-negativity:
g-t-/(g+t-+g-t-)
If gene and trait are negatively correlated:
- The sensitivity of using the absence of this gene as a diagnostic test to determine trait-positivity:
g-t+/(g+t++g-t+) - The specificity of using the presence of this gene as a diagnostic test to determine trait-negativity:
g+t-/(g+t-+g-t-)
Your data
I made a simple Excel that may make it easier to understand what is happening: SensSpecPlayground.xlsx
Ultramancc
Hi,
I'm currently using scoary2 and it's a useful tool. I have a question about sensitivity&specificity May I know the calculation way for those two values? As I have found there may be some conflicts with sensitivity and specificity, those genes were lowly detected in trait-positive but the results indicate they have a high sensitivity.