Hi Bioconductor community,

I performed a categorical analysis (control vs treated) using DESeq2, and I want to put together a figure where I show the average counts in the control and treated groups that includes error and a p value. To calculate counts of the treated group, do I simply multiply the log2 fc value (after first taking the anti-log2) by the base mean value (which is representative of control counts)? Do the standard error and adjusted p values only apply to the fc or can it be applied to counts?

Thanks!

There will be better replies I am sure, but I would just script that in R yourself i.e. calculation of mean counts for condition 1 versus 2 and standard error/ deviation whatever - it is a quick job even if you are a beginner. You just need to export the normalised counts from DESEQ then work from that. Then I am sure the p values apply to the counts because the fold change is calculated from the counts.