[BioC] edgeR contrast
Pickl, Julia
j.pickl at dkfz-heidelberg.de
Tue Sep 2 09:24:53 CEST 2014
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
[[alternative HTML version deleted]]
More information about the Bioconductor
mailing list