edgeR contrast

Hi all,

I try different contrasts to get a feeling for my data and also to find out the best contrast for my question. I would like to know what genes are enriched in IP.treat compared to IP.control, both adjusted for unspecific IgG binding.

So it seems like contrast 1 is the best: (IP.treat-IgG.treat)-(IP.control-IgG.control), however it seems like IgG.control is added to IP.treat as - and - is +. I then tried contrast 3 and 4, and get totally different results with genes only FC>1.

My question: Is it allowed to have more levels -1 than +1 or how can it be explained that contrast3 and 4 look very similar but totally different than contrast1 (and IP)?





Levels           IP contrast1 contrast2 contrast3 contrast4 contrast5



  IP.treat        1         1         1         1         1         0



  IP.control     -1        -1        -1        -1        -1         0



  IgG.treat       0        -1         0        -1        -1         1



  IgG.control     0         1         0        -1         0        -1





  subj            0         0         0         0         0         0


Thanks for any help.

Julia

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