I am using DESeq2 to estimate fold changes of treatment versus control in a time series experiment (with biological replicates). I am a little puzzled about the standard deviations of the fold changes provided by DESeq2. These are almost constant over all timepoints, although it doesn't look like this when I judge the biological replicates in the output of plotCounts. Can someone please enlighten me how the standard errors of the log2FC computed? I'd be especially interested how the standard errors of a contrast c("Condition_treatment_vs_ctrl") vs a contrast like c("Condition_treatment_vs_ctrl", "Time24.Conditiontreatment") are computed (in a setting with design=~ Time + Condition + Condition:Time) (Here the 2 standard errors are almost the same, which I would not expect when looking at the data).
I hope I managed to ask the question in an understandable way. Your help is very much appreciated!