Enter the body of text here Hi, there:
I read the previous posts about deriving confidence interval for fold change using DESeq result at URLs: 95% Confidence intervals for Fold Changes computed by DESeq2 and Error bars DESeq or DESeq2 fold change
one comment from Micheal Love mentioned: Estimated standard errors for the estimated coefficients on the log2 scale are given by the lfcSE column. Yes, you can convert these to fold change errors using this formula: 2^(coef - SE) and 2^(coef + SE).
If you multiple lfcSE by normal quantiles (e.g. qnorm(.025)), you can construct confidence intervals for the coefficients. ....
my concerning point that needs a bit clarification or confirmation is whether this referred to logFC or FC:
one of my own result table of an interested contrast from DESeq2 is shown below as an example:
SYMBOL baseMean log2FoldChange lfcSE pvalue padj
Igfbp3 6947.54841 7.586917789 0.323830741 2.08E-123 3.81E-119
Gap43 2411.144079 4.597075539 0.195529679 3.43E-123 3.81E-119
Bmp2 1134.843753 7.659549924 0.351744204 3.54E-107 2.62E-103
for gene Igfbp3, the log2FoldChange is 7.586917789, lfcSE is 0.323830741, so to derive 95% confidence internal (95%C.I.) accordinyl based on formula for 95%C.I., we can do following: [7.586917789-0.323830741qnorm(0.975), 7.586917789+0.323830741qnorm(0.975)] = [6.952221, 8.221614].
this calcualtion is based on logFC and and I read from the manual: The lfcSE gives the standard error of the log2FoldChange. and so the derived 95%C.I shall be for logFC, is my understanding correct? and for FC, shall be simple as 2^(6.952221) and 2^(8.221614)? just want to double check to make sure. also another question is: whether I used Log fold change shrinkage or not would impact the calculation or not? say if I do either res <- results(dds, contrast=Con1); or resLFC <- lfcShrink(dds, contrast = Con1, type="ashr"), the way of deriving 95% C.I for logFC would be different, or any concerns or issue?
Thanks so much for your help!
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