[BioC] edgeR contrast

[Julia [guest]]

I try different contrasts with edgeR 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    
 
 
  
 
 
Thanks for any help.
 
Julia

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