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The DESeq2 results table provides the fold change for each gene, but is there a way to get the confidence interval for each fold change the program generates ?
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Uh, that didn't work. I expected markdown symbols to work... Anyway, the CI is just β ± 1.96 x SE. And you have both the β and the SE
what do you mean by β ?
where did you get the 1.96 from ?
In this context β is the log fold change (it's the estimate of interest from your linear model, labeled as log2FoldChange in the output of
results. And the SE is labeled lfcSE. And the stat column is the ratio of the two, and is a Wald test). And since it's a Wald test, and assumes normality, 1.96 is the 97.5th percentile of a normal distribution. I am presuming by CI you mean a 95% CI.Put a different way, I got 1.96 from the first intro to stats class I took. If you don't already know something like that, it should be a big red flag to you. Analyzing these data is not the trickiest thing in the world (I do it, so how hard can it be?), but it's not the easiest thing either. You do have to know a bit about what you are doing if you want some assurance you are doing it right. So if you are missing some of the fundamentals I would recommend either filling in those blanks, or finding a local statistician to help (or at least to consult with).
ok thank you James for clarifying.