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

[Gordon K Smyth]

Dear Saad,

There isn't any way for us to tell what you might be doing wrong unless 
you show us the complete code you used.  We also need the actual output 
produced by topTags() or similar rather than your interpretation of it.

Best wishes
Gordon

> Date: Mon, 10 Oct 2011 12:41:30 -0700 (PDT)
> From: "saad khan [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, smk5g5 at mail.missouri.edu
> Subject: [BioC] EdgeR: Log FC does not changes when I swap the groups
>
>
> 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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