Hi all, 

I have searched for this high and low with no luck. I was wondering if it is possible (over a time course experiment) to filter genes that have a specific change across the time points. 

So for example, I would like to be able to look at genes that change from one time point to another only if it has a difference of a minimum change of 50 counts or more.  So if the change from one gene to another were 45 counts (for example), it would be rejected. Is there any way of doing this pre/post DDS and if so, would somebody be kind enough to share some code for this?

Many thanks!

In DESeq2, there is not a concept of filtering by absolute number of counts, instead we compute the fold change. You can specify a minimum fold change. See the vignette section about lfcThreshold.