Hello,

I'm plotting fitted curves for my genes of interest using logCPM, and I need to include the CI. I'm not sure how to do this using using the edgeR DEGlist. Do you have a recommendation on how to get the CI? I'm sorry for making such a basic question, but I'm not sure how to calculate it based on a negative binomial distribution.

CI= fitted mean +- margin error margin error = t_score * sterr t_score= qt(alpha/2, df, lower.tail=F) sterr = std/sqrt(n) std = sd(fit$fitted.values) ???

Best regards,

edgeR does not provide confidence intervals for fitted values. edgeR doesn't use t-statistics so the formula you give doesn't apply.

Note that fitted values are obtained from edgeR fit objects (DGEGLM class) rather than from DGEList objects.