Limma beta coefficient confidence intervals
1
0
Entering edit mode
fluentin44 • 0
@45f45212
Last seen 10 days ago
United Kingdom

Hi,

Has anyone any experince of extracting the beta coefficients form a limma object (i.e. fit_2) and calculating the 5% and 95% confidence intervals for the coefficients? Any help would be hugely appreciated.

fit <- lmFit(methylation_matrix, mod, method = "ls") # Use this line for full run, hash out for testing
fit_2 <- eBayes(fit)
table <- limma::topTable(fit_2, coef = 2, number = Inf)

Thanks,

Matt

limma limmaGUI beta • 189 views
ADD COMMENT
1
Entering edit mode
@james-w-macdonald-5106
Last seen 1 day ago
United States

see ?topTable.

You can simply add confint = TRUE

0
Entering edit mode

Unfortunately that returns the confidence intervals for logFC, not the B statistic.

ADD REPLY
0
Entering edit mode

You said beta in your original post, which is the logFC. You want the CI for the log odds?

ADD REPLY
0
Entering edit mode

Apologies, ive been a plank and obviously not read closely enough - in the toptable output logFC is essentially the effect size / B statistic for each individual regression per gene / CpG and B the log-odds?

ADD REPLY
1
Entering edit mode

It's not the effect size, which is a different thing. But it is the beta for the model you fit, estimating the difference between groups. The B statistic in that table is the log odds of being differentially expressed.

ADD REPLY
0
Entering edit mode

Ok much appreciated, thanks!

ADD REPLY

Login before adding your answer.

Traffic: 210 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6