[BioC] EdgeR: Log FC does not changes when I swap the groups

[saad khan [guest]]

I am running edgeR on RNA-seq data with two groups Control(C1,C2,C3) and Treated(P1,P2,P3) having three replicates each. I need the log FC ratio with Treated(P1,P2,P3) value in the numerator and Control(C1,C2,C3) in the denominator but the results I am getting with EdgeR are not well correlated with the read counts data that I have.

e.g.: 
for gene Glyma12g14980.1
 fold change (lg Fc) = 33.21571049
Read Count: Control 1= 20, Control2= 136, COntrol 3= 15, P1= 0, P2=  0, P3=  0

Glyma10g03970.1
Fold Change= -37.80306427
Read Count: Control1=0, Control2=0, Control 3=0, P1=  815, P2=1590, P3=1649

even when I swap the groups the result remain the same i.e.:  group<- c(rep(\"Control\",3),rep(\"Treated\",3)) and  group<- c(rep(\"Treated\",3),rep(\"Control\",3)) the results are the same.

Please suggest where I am going wrong.

Regards
Saad Khan
Graduate Student
University of Missouri

 -- output of sessionInfo(): 

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