Hi,

I'm using limma package to do differential expression analysis on a microarray data. May I know how the logFC is computed in the package?

I start the analysis with a normalized, log2 transformed dataset and a matrix indicate the case and groups as 
fit<- lmFit((normalized,log2transformed data), design).
cont.matrix<- makeContrasts(..., levels=design)
fit2 <- contrasts.fit(fit, cont.matrix)
fit2 <- eBayes(fit2)
result= topTable(fit2, adjust="BH", number=nrow(data))

A number of summary statistics are presented by topTable() for the top genes and the selected contrast. I manually compute the logFC for the 2 groups: G1mean=rowMeans(2^(normalized,log2transformed data in group1)), G2mean=rowMeans(2^(normalized,log2transformed data in group2)), FC=G2mean/G1mean, log2(FC).

The log2(FC) is not consistent with the one in the summary statistics output by topTable()...

Does the calculation of logFC depend on the variance?

Yuan
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