Question

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

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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(): *** -- Sent via the guest posting facility at bioconductor.org.

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ADD COMMENT • link updated 13.5 years ago by Gordon Smyth 52k • written 13.5 years ago by Guest User ★ 13k

score 0 · Answer 1 · 2011-10-13

Dear Saad,

You have apparently asked edgeR to compare the control group to the treatment group, and the log-fold-changes look to be in perfect agreement with your data, from what you have posted.

Note that the analysis done by edgeR does not depend on the order that the samples or treatments occur in your dataset. The comparison depends on what you asked for when you ran exactTest() or glmLRT().

It's hard to say more without knowing the code you have used or what you expected to see.

Best wishes
Gordon