[BioC] EdgeR analysis

[Mac449 [guest]]

Hi all,

I've been trying to perform a differential count analysis using Hi-C data. I have two replicates for one condition, and only one for the other comparison. The MA plot is not symmetric; there is a bias in one direction at higher average counts. I've tried to tune the normalized factors to change the shape of the plot with no success.

Best,
Mark

 -- output of sessionInfo(): 

sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] edgeR_3.4.2   limma_3.18.13

loaded via a namespace (and not attached):
[1] tools_3.0.2

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