co-expression analysis between LncRNA and mRNA based on P.value with function rcorr(x ,y , type=oearson) in R

Question

[yaghoub.amraei]

Hi all..

I have two sets of data, each of which has two treatments with two replications. The first group consisted of 2261 LncRNA (Long non-coding RNA) with FPKM each LncRNA and the second group consisted of 2261 genes with FPKM each of which genes. How can I calculate the p.value and correlation between these two data sets?

data set for genes with FPKM of 4 sample

Name    C1  C2  T1  T2
TRINITY_DN1460_c0_g1_i2 0   0   0.95061094  0.974081292
TRINITY_DN1445_c0_g1_i2 2.511946285 2.620287473 0   0.089860297
TRINITY_DN1453_c0_g1_i1 3.655753553 4.316118348 22.36035774 17.03695859
TRINITY_DN1442_c0_g1_i1 12.66961994 12.15529116 0.3557767   0.088292054
TRINITY_DN1441_c0_g1_i1 2.74152511  3.018707652 59.38689024 37.6744074 
TRINITY_DN9679_c0_g1_i1 0   0.053742144 0.056627791 44.57659804
TRINITY_DN9640_c0_g1_i1 0   0   0.903177433 0.896555518
TRINITY_DN9680_c0_g1_i1 4.781792659 3.733969417 22.6460333  40.55482311 
TRINITY_DN9600_c0_g1_i2 0   0   0.110793505 0.945838228
TRINITY_DN9653_c0_g1_i1 0.301219544 0   0.827706537 0.471431615
TRINITY_DN9647_c0_g1_i2 0.113683743 0   0.614529891 0.813365709 
TRINITY_DN8689_c0_g1_i1 0   0   3.633702889 6.890411988

data set for LncRNA with FPKM of 4 sample

 Name               C1               C2                  T1             T2
    LN.downTRINITY_DN1458_c0_g1_i1  0.358940548 0.675186832 0   0
    LN.downTRINITY_DN1454_c0_g1_i2  0.456895437 0.358485224 0.116225798 0
    LN.downTRINITY_DN9673_c0_g1_i1  0.380168215 0.66310871  0   0
    LN.downTRINITY_DN38727_c0_g1_i1 0.450390369 0.231056988 0   0
    LN.downTRINITY_DN38736_c0_g1_i1 0.561200698 0.959681139 0   0
    LN.downTRINITY_DN38799_c0_g1_i1 0.267845788 0.549635562 0   0
    LN.downTRINITY_DN38710_c0_g1_i1 0.572892379 0.167944199 0   0
    LN.downTRINITY_DN38745_c0_g1_i1 0.733709862 0.84690927  0.09915372  0
    LN.downTRINITY_DN35286_c0_g1_i1 0.231650411 0.297100304 0   0
    LN.downTRINITY_DN35228_c0_g1_i1 0.356048781 0.438380025 0.076986423 0
    LN.downTRINITY_DN35254_c0_g1_i1 0.681789277 0.099933738 0   0
    LN.downTRINITY_DN8671_c0_g1_i1  0.305316442 0.501222067 0   0

[Ram]

Your formatting was quite messed up - it looked like you selected the text and experimented with a few buttons. I've cleaned it up for you now. For future reference, code formatting is done using the 101010 button

[Kevin Blighe]

What have you tried already ... ?