[BioC] Are the logFC confidence intervals returned by topTable adjusted for multiple comparisons?

Calin-Jageman, Robert rcalinjageman at dom.edu
Thu Aug 14 18:04:13 CEST 2014

I'm using limma to analyze both microarray and qPCR data.  For logFC values, I'd like to report CIs.  I found that this feature was added to topTable around 2011 (https://stat.ethz.ch/pipermail/bioconductor/2011-January/037579.html )

I'm wondering, though: are the CIs produced by topTable expanded for the multiple comparison method selected?  Or are these uncorrected/standard CIs for each transcript?

For reference, I used:
                fit <- lmFit(qpcr_1hr)
fit2 <- eBayes(fit)
regulated <- topTable(fit2, adjust="BH", confint=TRUE,number=nrow(fit2))

So I was expected the CIs to also be adjusted based on Benjamini-Hochberg (as discussed in Jung, Friede, and Biebarth, 2011 - http://www.biomedcentral.com/1471-2105/12/288 ).  But looking at the CIs I'm getting, they seem more likely to be uncorrected.

Does anyone know for sure?



Bob Calin-Jageman
Neuroscience Program Director
Associate Professor
Department of Psychology
210 Parmer Hall
Dominican University
7900 West Division
River Forest, IL 60305
rcalinjageman at dom.edu<mailto:rcalinjageman at dom.edu>

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