Hi, 
Try: 
##Assuming X and Y are matrices (as stated) 
Y[!Y %in% X,,drop=FALSE] 
#     numberall 
#[1,] "gen3"   
#[2,] "gen4"   
#[3,] "genx4"   
A.K. 


I would like to exclude entire lines in matrix "Y" based in 2 collumns in 
matrix "X": 

Matrix "X": 

  number1  number2 
   gen1     genx1   
   gen1     genx2 
   gen2     genx3 
   gen2     genx5 

Matrix "Y": 

   numberall 
    gen1 
    genx1 
    gen2 
    genx2 
    gen3 
    genx3 
    gen4 
    genx4 

Expected output matrix 

   numberall 
    gen3 
    gen4 
    gen4x 

Cheers.

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