correlation between element-gene

Question

[Chironex]

I have two matrix identical in N° of rows and columns. In the first matrix rows indicate transposable elements and columns indicate samples. the matrix show the degree of expression of each element in samples:

M1 <-


            elements          ova       testes       retina   optic_lobe       suckers 
1   LINES/3           1.473559e+03   962.953589   673.903449   558.879946   947.631992          
2   SINES             1.836210e+02   355.808323   577.807528   341.048786   99.902702          
3  DNA TRANSP         9.181051e+00   178.661200  4387.148414    53.907711   353.413028

In Second matrix rows indicate genes and columns indicate samples. the matrix show the degree of expression of each gene in samples:

 M2 <-
            elements          ova       testes       retina   optic_lobe  suckers 
1   OCBIM_22028242mg 1.473559e+03   962.953589   673.903449   558.879946   947.631992          
2   OCBIM_22008718mg 1.836210e+02   355.808323   577.807528   341.048786   99.902702          
3   OCBIM_22009482mg 9.181051e+00   178.661200  4387.148414    53.907711   353.413028

I have to make an element-gene correlation. I have to check, for example, if the element A expressed much in the tissue X has the corresponding gene A expressed very, little, or nothing in the tissue X. fOR example I'm expecting this result:

M1,2 <-
                elements          ova       testes       retina   optic_lobe  suckers 
    1   TE/ gene1                  0.3          1          0.5         -1         0.3          
    2   TE/gene2                   0.1        0.6            0         -1         0.9      
    3   TE/gene3                     1          1          0.8        -0.2       -0.3

[Kevin Blighe]

Hey, can you specifically state what you want to correlate? It is not clear from that M1,2 output that you are showing.