edgeR contrast
"Julia [guest]" <[email protected]> Tue, 2 Sep 2014 03:42:13 -0700 (PDT)
| Newsgroups | gmane.science.biology.informatics.conductor |
|---|---|
| Message-ID | <[email protected]> |
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 â and â 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 -- output of sessionInfo(): . -- Sent via the guest posting facility at bioconductor.org. _______________________________________________ Bioconductor mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor