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 -- Sent via the guest posting facility at bioconductor.org.