Table 2 

The number of functional class whose F1 = NaN for four algorithms and four functional groups 

algorithms 
< 60 
60100 
100300 
> 300 


twoclass 
31 
8 
3 
1 
twoclassbal 
0 
0 
0 
0 
PSoL 
22 
6 
0 
1 
SPERNE 
0 
0 
0 
0 


When the number of negative examples is far more than positive examples, imbalanced problem occurs and the algorithm can not recall any true positive examples for some functional classes. As a result, P = 0 and R = 0 result in F1 = NaN (Not a Number) in matlab. Table 2 shows the number of NaN for each functional group. 

Chen et al. BMC Genomics 2010 11(Suppl 2):S11 doi:10.1186/1471216411S2S11 